Starting phenix.real_space_refine on Thu Mar 5 04:57:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t75_25734/03_2026/7t75_25734.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t75_25734/03_2026/7t75_25734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t75_25734/03_2026/7t75_25734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t75_25734/03_2026/7t75_25734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t75_25734/03_2026/7t75_25734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t75_25734/03_2026/7t75_25734.map" } resolution = 2.7 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= 0.049 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 120 5.16 5 C 12024 2.51 5 N 3207 2.21 5 O 3876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 19227 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 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: "J" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "K" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "M" 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: "N" 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: "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: 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: "Q" 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: "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: "S" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "V" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "W" 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: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" 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: "1" 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: "2" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "3" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.12, per 1000 atoms: 0.21 Number of scatterers: 19227 At special positions: 0 Unit cell: (124.63, 128.75, 149.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3876 8.00 N 3207 7.00 C 12024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 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=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.06 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.05 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.05 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.04 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.02 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.02 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS U 119 " - pdb=" SG CYS U 205 " distance=2.06 Simple disulfide: pdb=" SG CYS U 126 " - pdb=" SG CYS U 196 " distance=2.05 Simple disulfide: pdb=" SG CYS U 131 " - pdb=" SG CYS U 157 " distance=2.04 Simple disulfide: pdb=" SG CYS U 218 " - pdb=" SG CYS U 247 " distance=2.05 Simple disulfide: pdb=" SG CYS U 228 " - pdb=" SG CYS U 239 " distance=2.03 Simple disulfide: pdb=" SG CYS U 296 " - pdb=" SG CYS U 331 " distance=2.03 Simple disulfide: pdb=" SG CYS U 378 " - pdb=" SG CYS U 445 " distance=2.04 Simple disulfide: pdb=" SG CYS U 385 " - pdb=" SG CYS U 418 " distance=2.02 Simple disulfide: pdb=" SG CYS U 501 " - pdb=" SG CYS V 605 " distance=2.02 Simple disulfide: pdb=" SG CYS V 598 " - pdb=" SG CYS V 604 " distance=2.02 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.02 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 0 3 " - " MAN 0 4 " " BMA E 3 " - " MAN E 4 " " BMA Q 3 " - " MAN Q 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " BETA1-6 " NAG 2 1 " - " FUC 2 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG 3 1 " - " FUC 3 2 " " NAG G 1 " - " FUC G 2 " " NAG I 1 " - " FUC I 2 " " NAG S 1 " - " FUC S 2 " " NAG T 1 " - " FUC T 2 " NAG-ASN " NAG 0 1 " - " ASN U 262 " " NAG 1 1 " - " ASN U 156 " " NAG 2 1 " - " ASN V 618 " " NAG 3 1 " - " ASN V 611 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 355 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 197 " " NAG A 613 " - " ASN A 133 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 637 " " NAG C 1 " - " ASN A 386 " " NAG D 1 " - " ASN A 332 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 156 " " NAG G 1 " - " ASN B 618 " " NAG I 1 " - " ASN B 611 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 160 " " NAG J 603 " - " ASN J 234 " " NAG J 604 " - " ASN J 137 " " NAG J 605 " - " ASN J 355 " " NAG J 606 " - " ASN J 276 " " NAG J 607 " - " ASN J 392 " " NAG J 608 " - " ASN J 339 " " NAG J 609 " - " ASN J 295 " " NAG J 610 " - " ASN J 448 " " NAG J 611 " - " ASN J 301 " " NAG J 612 " - " ASN J 197 " " NAG J 613 " - " ASN J 133 " " NAG K 701 " - " ASN K 625 " " NAG K 702 " - " ASN K 637 " " NAG O 1 " - " ASN J 386 " " NAG P 1 " - " ASN J 332 " " NAG Q 1 " - " ASN J 262 " " NAG R 1 " - " ASN J 156 " " NAG S 1 " - " ASN K 618 " " NAG T 1 " - " ASN K 611 " " NAG U 601 " - " ASN U 88 " " NAG U 602 " - " ASN U 160 " " NAG U 603 " - " ASN U 234 " " NAG U 604 " - " ASN U 137 " " NAG U 605 " - " ASN U 355 " " NAG U 606 " - " ASN U 276 " " NAG U 607 " - " ASN U 392 " " NAG U 608 " - " ASN U 339 " " NAG U 609 " - " ASN U 295 " " NAG U 610 " - " ASN U 448 " " NAG U 611 " - " ASN U 301 " " NAG U 612 " - " ASN U 197 " " NAG U 613 " - " ASN U 133 " " NAG V 701 " - " ASN V 625 " " NAG V 702 " - " ASN V 637 " " NAG Y 1 " - " ASN U 386 " " NAG Z 1 " - " ASN U 332 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 899.2 milliseconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 20.3% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.554A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 4.085A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.412A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 534 through 540 removed outlier: 3.524A pdb=" N GLN B 538 " --> pdb=" O THR B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 659 removed outlier: 3.740A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (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 'J' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 143 Processing helix chain 'J' and resid 335 through 350 Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.554A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 484 removed outlier: 4.084A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 521 through 526 removed outlier: 4.412A pdb=" N GLY K 525 " --> pdb=" O GLY K 522 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 532 Processing helix chain 'K' and resid 534 through 540 removed outlier: 3.524A pdb=" N GLN K 538 " --> pdb=" O THR K 534 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 596 Processing helix chain 'K' and resid 618 through 624 Processing helix chain 'K' and resid 627 through 636 Processing helix chain 'K' and resid 638 through 659 removed outlier: 3.740A pdb=" N LYS K 655 " --> pdb=" O ASN K 651 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP K 659 " --> pdb=" O LYS K 655 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'U' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU U 102 " --> pdb=" O ASN U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 143 Processing helix chain 'U' and resid 335 through 350 Processing helix chain 'U' and resid 368 through 373 removed outlier: 3.555A pdb=" N THR U 373 " --> pdb=" O LEU U 369 " (cutoff:3.500A) Processing helix chain 'U' and resid 475 through 484 removed outlier: 4.085A pdb=" N GLU U 482 " --> pdb=" O ASN U 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 521 through 526 removed outlier: 4.412A pdb=" N GLY V 525 " --> pdb=" O GLY V 522 " (cutoff:3.500A) Processing helix chain 'V' and resid 527 through 532 Processing helix chain 'V' and resid 534 through 540 removed outlier: 3.524A pdb=" N GLN V 538 " --> pdb=" O THR V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 572 through 596 Processing helix chain 'V' and resid 618 through 624 Processing helix chain 'V' and resid 627 through 636 Processing helix chain 'V' and resid 638 through 659 removed outlier: 3.740A pdb=" N LYS V 655 " --> pdb=" O ASN V 651 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP V 659 " --> pdb=" O LYS V 655 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 32 Processing helix chain 'W' and resid 61 through 64 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'X' and resid 79 through 83 Processing sheet with id=1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.332A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.678A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 53 through 55 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 201 through 203 removed outlier: 6.405A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.898A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=9, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100H through 103 Processing sheet with id=10, first strand: chain 'L' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 12 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=10 Processing sheet with id=11, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=12, first strand: chain 'J' and resid 494 through 499 removed outlier: 5.332A pdb=" N VAL K 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL J 38 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR K 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR J 40 " --> pdb=" O CYS K 604 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS K 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.678A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=15, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=16, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=17, first strand: chain 'J' and resid 201 through 203 removed outlier: 6.404A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'J' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 259 through 261 current: chain 'J' and resid 284 through 312 removed outlier: 6.898A pdb=" N ASN J 301 " --> pdb=" O ILE J 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE J 323 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 315 through 323A current: chain 'J' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 381 through 385 current: chain 'J' and resid 466 through 470 Processing sheet with id=19, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=20, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=21, first strand: chain 'N' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 12 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=23, first strand: chain 'U' and resid 494 through 499 removed outlier: 5.333A pdb=" N VAL V 608 " --> pdb=" O VAL U 36 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL U 38 " --> pdb=" O THR V 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR V 606 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR U 40 " --> pdb=" O CYS V 604 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS V 604 " --> pdb=" O TYR U 40 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'U' and resid 45 through 47 removed outlier: 3.678A pdb=" N ILE U 225 " --> pdb=" O VAL U 245 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'U' and resid 53 through 55 Processing sheet with id=26, first strand: chain 'U' and resid 91 through 94 Processing sheet with id=27, first strand: chain 'U' and resid 169 through 177 Processing sheet with id=28, first strand: chain 'U' and resid 201 through 203 removed outlier: 6.406A pdb=" N THR U 202 " --> pdb=" O TYR U 435 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'U' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 259 through 261 current: chain 'U' and resid 284 through 312 removed outlier: 6.898A pdb=" N ASN U 301 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE U 323 " --> pdb=" O ASN U 301 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR U 303 " --> pdb=" O GLY U 321 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN U 315 " --> pdb=" O ILE U 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 315 through 323A current: chain 'U' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 381 through 385 current: chain 'U' and resid 466 through 470 Processing sheet with id=30, first strand: chain 'W' and resid 3 through 6 Processing sheet with id=31, first strand: chain 'W' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 11 through 12 current: chain 'W' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 57 through 59 current: chain 'W' and resid 100H through 103 Processing sheet with id=32, first strand: chain 'X' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 12 through 13 current: chain 'X' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 45 through 48 current: chain 'X' and resid 96 through 98 No H-bonds generated for sheet with id=32 Processing sheet with id=33, first strand: chain 'X' and resid 19 through 24 516 hydrogen bonds defined for protein. 1368 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: 3.85 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3288 1.31 - 1.45: 5878 1.45 - 1.58: 10172 1.58 - 1.72: 101 1.72 - 1.86: 160 Bond restraints: 19599 Sorted by residual: bond pdb=" CB ASP L 27B" pdb=" CG ASP L 27B" ideal model delta sigma weight residual 1.516 1.355 0.161 2.50e-02 1.60e+03 4.13e+01 bond pdb=" CB ASP N 27B" pdb=" CG ASP N 27B" ideal model delta sigma weight residual 1.516 1.355 0.161 2.50e-02 1.60e+03 4.12e+01 bond pdb=" CB ASP X 27B" pdb=" CG ASP X 27B" ideal model delta sigma weight residual 1.516 1.356 0.160 2.50e-02 1.60e+03 4.12e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.85e+01 bond pdb=" NE ARG J 503 " pdb=" CZ ARG J 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.84e+01 ... (remaining 19594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.80: 26544 7.80 - 15.60: 39 15.60 - 23.40: 0 23.40 - 31.20: 0 31.20 - 39.00: 3 Bond angle restraints: 26586 Sorted by residual: angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 163.56 -39.00 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C2 NAG Z 1 " pdb=" N2 NAG Z 1 " pdb=" C7 NAG Z 1 " ideal model delta sigma weight residual 124.56 163.53 -38.97 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " pdb=" C7 NAG D 1 " ideal model delta sigma weight residual 124.56 163.53 -38.97 3.00e+00 1.11e-01 1.69e+02 angle pdb=" N GLU J 87 " pdb=" CA GLU J 87 " pdb=" C GLU J 87 " ideal model delta sigma weight residual 111.33 121.04 -9.71 1.21e+00 6.83e-01 6.44e+01 angle pdb=" N GLU U 87 " pdb=" CA GLU U 87 " pdb=" C GLU U 87 " ideal model delta sigma weight residual 111.33 121.03 -9.70 1.21e+00 6.83e-01 6.43e+01 ... (remaining 26581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 12357 22.10 - 44.20: 318 44.20 - 66.30: 84 66.30 - 88.40: 36 88.40 - 110.50: 12 Dihedral angle restraints: 12807 sinusoidal: 6180 harmonic: 6627 Sorted by residual: dihedral pdb=" C ASN B 637 " pdb=" N ASN B 637 " pdb=" CA ASN B 637 " pdb=" CB ASN B 637 " ideal model delta harmonic sigma weight residual -122.60 -111.59 -11.01 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" C ASN K 637 " pdb=" N ASN K 637 " pdb=" CA ASN K 637 " pdb=" CB ASN K 637 " ideal model delta harmonic sigma weight residual -122.60 -111.61 -10.99 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" C ASN V 637 " pdb=" N ASN V 637 " pdb=" CA ASN V 637 " pdb=" CB ASN V 637 " ideal model delta harmonic sigma weight residual -122.60 -111.61 -10.99 0 2.50e+00 1.60e-01 1.93e+01 ... (remaining 12804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2149 0.104 - 0.209: 676 0.209 - 0.313: 252 0.313 - 0.418: 94 0.418 - 0.522: 54 Chirality restraints: 3225 Sorted by residual: chirality pdb=" C1 FUC T 2 " pdb=" O6 NAG T 1 " pdb=" C2 FUC T 2 " pdb=" O5 FUC T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 FUC I 2 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 2 " pdb=" O5 FUC I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 FUC 3 2 " pdb=" O6 NAG 3 1 " pdb=" C2 FUC 3 2 " pdb=" O5 FUC 3 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.34e+02 ... (remaining 3222 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 702 " -0.263 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" C7 NAG V 702 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG V 702 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG V 702 " 0.413 2.00e-02 2.50e+03 pdb=" O7 NAG V 702 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 702 " 0.263 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" C7 NAG K 702 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG K 702 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG K 702 " -0.413 2.00e-02 2.50e+03 pdb=" O7 NAG K 702 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " -0.263 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" C7 NAG B 702 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " -0.031 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " 0.413 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.171 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4205 2.80 - 3.32: 16580 3.32 - 3.85: 31609 3.85 - 4.37: 39357 4.37 - 4.90: 63668 Nonbonded interactions: 155419 Sorted by model distance: nonbonded pdb=" NH2 ARG M 53 " pdb=" OD1 ASN V 656 " model vdw 2.271 3.120 nonbonded pdb=" OD1 ASN B 656 " pdb=" NH2 ARG W 53 " model vdw 2.272 3.120 nonbonded pdb=" NH2 ARG H 53 " pdb=" OD1 ASN K 656 " model vdw 2.272 3.120 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.371 3.120 nonbonded pdb=" N ASP H 84 " pdb=" OD1 ASP H 84 " model vdw 2.371 3.120 ... (remaining 155414 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: 0.04 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'E' selection = chain 'Q' } ncs_group { reference = (chain '1' and resid 1) selection = (chain '2' and resid 1) selection = (chain '3' and resid 1) selection = (chain 'C' and resid 1) selection = (chain 'D' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) } ncs_group { reference = chain 'A' selection = chain 'J' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'K' selection = chain 'V' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'X' } 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: 4.630 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.690 Find NCS groups from input model: 0.660 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: 0.010 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.022 0.161 19722 Z= 1.177 Angle : 1.850 38.997 26919 Z= 1.177 Chirality : 0.139 0.522 3225 Planarity : 0.014 0.234 3276 Dihedral : 11.787 110.504 8451 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.79 % Allowed : 2.51 % Favored : 96.69 % Rotamer: Outliers : 0.90 % Allowed : 0.85 % Favored : 98.26 % Cbeta Deviations : 0.56 % 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: 0.58 (0.17), residues: 2268 helix: -0.64 (0.24), residues: 372 sheet: 0.90 (0.20), residues: 714 loop : 0.58 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 71 TYR 0.064 0.008 TYR L 96 PHE 0.040 0.007 PHE A 353 TRP 0.050 0.009 TRP J 96 HIS 0.012 0.003 HIS J 85 Details of bonding type rmsd covalent geometry : bond 0.02209 (19599) covalent geometry : angle 1.82657 (26586) SS BOND : bond 0.01349 ( 36) SS BOND : angle 3.28449 ( 72) hydrogen bonds : bond 0.17588 ( 516) hydrogen bonds : angle 6.64987 ( 1368) link_ALPHA1-3 : bond 0.07667 ( 3) link_ALPHA1-3 : angle 3.97063 ( 9) link_BETA1-4 : bond 0.07157 ( 15) link_BETA1-4 : angle 4.76798 ( 45) link_BETA1-6 : bond 0.05219 ( 6) link_BETA1-6 : angle 2.60889 ( 18) link_NAG-ASN : bond 0.06887 ( 63) link_NAG-ASN : angle 2.69601 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 414 time to evaluate : 0.937 Fit side-chains REVERT: A 142 MET cc_start: 0.6882 (mmm) cc_final: 0.6439 (mmm) REVERT: L 94 ARG cc_start: 0.6858 (mmm160) cc_final: 0.5554 (mtt180) REVERT: N 94 ARG cc_start: 0.6826 (mmm160) cc_final: 0.5335 (mtt-85) REVERT: U 142 MET cc_start: 0.6788 (mmm) cc_final: 0.6543 (mmm) REVERT: X 94 ARG cc_start: 0.6982 (mmm160) cc_final: 0.5462 (ptp-170) outliers start: 18 outliers final: 4 residues processed: 426 average time/residue: 0.8002 time to fit residues: 373.4413 Evaluate side-chains 231 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain U residue 189 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 280 ASN A 302 ASN A 348 GLN B 652 GLN H 100BGLN H 105 GLN J 280 ASN J 302 ASN J 348 GLN K 653 GLN M 100BGLN U 302 ASN U 348 GLN V 630 GLN V 653 GLN X 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112158 restraints weight = 22163.707| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.17 r_work: 0.3173 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19722 Z= 0.150 Angle : 0.703 10.906 26919 Z= 0.348 Chirality : 0.047 0.252 3225 Planarity : 0.004 0.052 3276 Dihedral : 8.713 75.363 4277 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.47 % Favored : 97.13 % Rotamer: Outliers : 3.09 % Allowed : 9.67 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.60 (0.17), residues: 2268 helix: 1.21 (0.27), residues: 375 sheet: 0.64 (0.19), residues: 723 loop : 0.08 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 143 TYR 0.011 0.001 TYR M 100G PHE 0.016 0.002 PHE A 176 TRP 0.023 0.002 TRP J 479 HIS 0.004 0.001 HIS J 85 Details of bonding type rmsd covalent geometry : bond 0.00331 (19599) covalent geometry : angle 0.64735 (26586) SS BOND : bond 0.00248 ( 36) SS BOND : angle 1.49131 ( 72) hydrogen bonds : bond 0.04970 ( 516) hydrogen bonds : angle 4.85581 ( 1368) link_ALPHA1-3 : bond 0.01363 ( 3) link_ALPHA1-3 : angle 2.24067 ( 9) link_BETA1-4 : bond 0.00565 ( 15) link_BETA1-4 : angle 2.58072 ( 45) link_BETA1-6 : bond 0.00613 ( 6) link_BETA1-6 : angle 0.97129 ( 18) link_NAG-ASN : bond 0.00299 ( 63) link_NAG-ASN : angle 2.94943 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 252 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8949 (mtp) cc_final: 0.8698 (mtp) REVERT: A 142 MET cc_start: 0.6345 (mmm) cc_final: 0.5717 (mmm) REVERT: L 94 ARG cc_start: 0.7309 (mmm160) cc_final: 0.4806 (mtt180) REVERT: J 97 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7948 (mttt) REVERT: J 166 ARG cc_start: 0.7967 (mtp-110) cc_final: 0.7693 (mtm110) REVERT: J 208 VAL cc_start: 0.6755 (t) cc_final: 0.6370 (p) REVERT: M 23 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6648 (tmt170) REVERT: N 94 ARG cc_start: 0.7204 (mmm160) cc_final: 0.4703 (mtt-85) REVERT: U 83 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: U 97 LYS cc_start: 0.8332 (mmtt) cc_final: 0.7993 (mttp) REVERT: U 102 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7618 (mp0) REVERT: U 106 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: U 143 ARG cc_start: 0.6546 (tpp-160) cc_final: 0.6026 (mtp85) REVERT: U 348 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.6637 (mp-120) REVERT: W 23 ARG cc_start: 0.8313 (tmt170) cc_final: 0.8021 (tmt170) REVERT: W 100 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8317 (p) REVERT: X 94 ARG cc_start: 0.7163 (mmm160) cc_final: 0.4635 (mtt180) REVERT: X 103 ARG cc_start: 0.7657 (tpp-160) cc_final: 0.7427 (tpp-160) outliers start: 62 outliers final: 30 residues processed: 297 average time/residue: 0.7499 time to fit residues: 245.4238 Evaluate side-chains 235 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 83 GLU Chi-restraints excluded: chain U residue 106 GLU Chi-restraints excluded: chain U residue 138 ILE Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 348 GLN Chi-restraints excluded: chain U residue 371 VAL Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 128 optimal weight: 7.9990 chunk 164 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 170 optimal weight: 0.0770 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN B 653 GLN H 105 GLN L 31 ASN J 283 ASN J 348 GLN K 653 GLN U 283 ASN X 95 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113668 restraints weight = 22472.027| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.03 r_work: 0.3207 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19722 Z= 0.123 Angle : 0.600 9.501 26919 Z= 0.299 Chirality : 0.045 0.269 3225 Planarity : 0.004 0.044 3276 Dihedral : 7.272 59.898 4277 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.91 % Favored : 96.87 % Rotamer: Outliers : 3.09 % Allowed : 10.56 % Favored : 86.35 % 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: 0.66 (0.18), residues: 2268 helix: 2.05 (0.27), residues: 357 sheet: 0.64 (0.19), residues: 717 loop : -0.13 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 143 TYR 0.019 0.001 TYR A 173 PHE 0.013 0.002 PHE M 29 TRP 0.020 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00276 (19599) covalent geometry : angle 0.56627 (26586) SS BOND : bond 0.00562 ( 36) SS BOND : angle 1.11525 ( 72) hydrogen bonds : bond 0.04244 ( 516) hydrogen bonds : angle 4.40770 ( 1368) link_ALPHA1-3 : bond 0.01344 ( 3) link_ALPHA1-3 : angle 1.10190 ( 9) link_BETA1-4 : bond 0.00642 ( 15) link_BETA1-4 : angle 1.94442 ( 45) link_BETA1-6 : bond 0.00432 ( 6) link_BETA1-6 : angle 1.18343 ( 18) link_NAG-ASN : bond 0.00288 ( 63) link_NAG-ASN : angle 2.13600 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 218 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8923 (mtp) cc_final: 0.8551 (mtp) REVERT: A 142 MET cc_start: 0.6401 (mmm) cc_final: 0.5650 (mmm) REVERT: A 153 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7079 (mt-10) REVERT: A 208 VAL cc_start: 0.6517 (t) cc_final: 0.6226 (p) REVERT: A 412 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6854 (t0) REVERT: B 533 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8713 (mtt) REVERT: L 94 ARG cc_start: 0.7193 (mmm160) cc_final: 0.4654 (mtt-85) REVERT: J 97 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7862 (mttt) REVERT: J 106 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: J 166 ARG cc_start: 0.7877 (mtp-110) cc_final: 0.7493 (mtm110) REVERT: J 208 VAL cc_start: 0.6698 (t) cc_final: 0.6308 (p) REVERT: K 616 ASN cc_start: 0.8390 (p0) cc_final: 0.7955 (t0) REVERT: M 23 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6566 (tmt170) REVERT: N 94 ARG cc_start: 0.7070 (mmm160) cc_final: 0.4541 (mtt-85) REVERT: U 49 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8341 (mt-10) REVERT: U 97 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7885 (mttp) REVERT: U 143 ARG cc_start: 0.6413 (tpp-160) cc_final: 0.5939 (mtp85) REVERT: U 153 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7454 (mm-30) REVERT: X 94 ARG cc_start: 0.7136 (mmm160) cc_final: 0.4690 (mtt180) outliers start: 62 outliers final: 28 residues processed: 261 average time/residue: 0.7348 time to fit residues: 212.1124 Evaluate side-chains 229 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain U residue 138 ILE Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 371 VAL Chi-restraints excluded: chain U residue 375 SER Chi-restraints excluded: chain V residue 536 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 188 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 170 optimal weight: 3.9990 chunk 144 optimal weight: 0.2980 chunk 201 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN J 348 GLN N 31 ASN U 348 GLN X 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110836 restraints weight = 22253.759| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.04 r_work: 0.3169 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19722 Z= 0.150 Angle : 0.608 9.581 26919 Z= 0.303 Chirality : 0.046 0.265 3225 Planarity : 0.004 0.035 3276 Dihedral : 6.329 59.494 4277 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.04 % Favored : 96.74 % Rotamer: Outliers : 3.84 % Allowed : 10.41 % Favored : 85.75 % 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: 0.57 (0.18), residues: 2268 helix: 2.11 (0.27), residues: 360 sheet: 0.66 (0.19), residues: 717 loop : -0.30 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 143 TYR 0.019 0.001 TYR A 173 PHE 0.016 0.002 PHE M 29 TRP 0.023 0.002 TRP J 479 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00354 (19599) covalent geometry : angle 0.58002 (26586) SS BOND : bond 0.00524 ( 36) SS BOND : angle 1.14670 ( 72) hydrogen bonds : bond 0.04526 ( 516) hydrogen bonds : angle 4.38920 ( 1368) link_ALPHA1-3 : bond 0.01206 ( 3) link_ALPHA1-3 : angle 1.27652 ( 9) link_BETA1-4 : bond 0.00483 ( 15) link_BETA1-4 : angle 1.88874 ( 45) link_BETA1-6 : bond 0.00327 ( 6) link_BETA1-6 : angle 1.25946 ( 18) link_NAG-ASN : bond 0.00221 ( 63) link_NAG-ASN : angle 1.93225 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 205 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8220 (mtmt) REVERT: A 142 MET cc_start: 0.6411 (mmm) cc_final: 0.5963 (mmm) REVERT: A 208 VAL cc_start: 0.6504 (t) cc_final: 0.6207 (p) REVERT: A 335 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7340 (ttpt) REVERT: A 412 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6427 (t0) REVERT: A 428 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6543 (mt0) REVERT: B 533 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8765 (mtt) REVERT: B 633 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8181 (mtpt) REVERT: L 94 ARG cc_start: 0.7160 (mmm160) cc_final: 0.4595 (mtt-85) REVERT: J 97 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7950 (mttt) REVERT: J 106 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: J 166 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7578 (mtm110) REVERT: J 208 VAL cc_start: 0.6558 (t) cc_final: 0.6238 (p) REVERT: M 23 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.6585 (tmt170) REVERT: N 85 ASP cc_start: 0.8481 (m-30) cc_final: 0.8268 (m-30) REVERT: N 94 ARG cc_start: 0.6985 (mmm160) cc_final: 0.4446 (mtt-85) REVERT: N 103 ARG cc_start: 0.8224 (tpp80) cc_final: 0.8004 (tpp-160) REVERT: U 49 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8338 (mt-10) REVERT: U 97 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7911 (mttp) REVERT: U 143 ARG cc_start: 0.6543 (tpp-160) cc_final: 0.6050 (mtp85) REVERT: U 153 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7424 (mm-30) REVERT: W 100 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8800 (mt0) REVERT: X 27 ASP cc_start: 0.7370 (m-30) cc_final: 0.7125 (m-30) REVERT: X 94 ARG cc_start: 0.7024 (mmm160) cc_final: 0.4568 (mtt-85) outliers start: 77 outliers final: 37 residues processed: 264 average time/residue: 0.7665 time to fit residues: 223.2043 Evaluate side-chains 241 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 364 SER Chi-restraints excluded: chain J residue 388 SER Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain U residue 138 ILE Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 364 SER Chi-restraints excluded: chain U residue 371 VAL Chi-restraints excluded: chain U residue 388 SER Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 612 SER Chi-restraints excluded: chain W residue 100 GLN Chi-restraints excluded: chain X residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 348 GLN J 348 GLN J 363 GLN U 348 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116132 restraints weight = 22025.809| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.72 r_work: 0.3032 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19722 Z= 0.198 Angle : 0.660 10.012 26919 Z= 0.329 Chirality : 0.047 0.263 3225 Planarity : 0.004 0.036 3276 Dihedral : 6.224 59.098 4277 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.31 % Favored : 96.47 % Rotamer: Outliers : 3.19 % Allowed : 11.56 % Favored : 85.25 % 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: 2268 helix: 1.67 (0.27), residues: 378 sheet: 0.63 (0.19), residues: 723 loop : -0.39 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 143 TYR 0.021 0.002 TYR A 173 PHE 0.016 0.002 PHE M 29 TRP 0.029 0.002 TRP J 479 HIS 0.006 0.002 HIS U 352 Details of bonding type rmsd covalent geometry : bond 0.00478 (19599) covalent geometry : angle 0.63219 (26586) SS BOND : bond 0.00583 ( 36) SS BOND : angle 1.24685 ( 72) hydrogen bonds : bond 0.05138 ( 516) hydrogen bonds : angle 4.48774 ( 1368) link_ALPHA1-3 : bond 0.01064 ( 3) link_ALPHA1-3 : angle 1.08830 ( 9) link_BETA1-4 : bond 0.00426 ( 15) link_BETA1-4 : angle 1.82267 ( 45) link_BETA1-6 : bond 0.00248 ( 6) link_BETA1-6 : angle 1.41744 ( 18) link_NAG-ASN : bond 0.00224 ( 63) link_NAG-ASN : angle 2.06087 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8438 (mtmt) REVERT: A 142 MET cc_start: 0.6350 (mmm) cc_final: 0.5955 (mmm) REVERT: A 335 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7418 (ttpt) REVERT: A 360 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7183 (ttp80) REVERT: A 412 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6481 (t0) REVERT: B 533 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8866 (mtp) REVERT: B 633 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8272 (mtpt) REVERT: L 94 ARG cc_start: 0.7258 (mmm160) cc_final: 0.4629 (mtt180) REVERT: L 103 ARG cc_start: 0.8293 (tpp-160) cc_final: 0.8085 (tpp-160) REVERT: J 97 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8098 (mttm) REVERT: J 106 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: J 166 ARG cc_start: 0.8073 (mtp-110) cc_final: 0.7816 (mtm110) REVERT: J 246 GLN cc_start: 0.7262 (pt0) cc_final: 0.6543 (pm20) REVERT: M 34 MET cc_start: 0.9197 (mtp) cc_final: 0.8835 (mtp) REVERT: N 85 ASP cc_start: 0.8584 (m-30) cc_final: 0.8368 (m-30) REVERT: N 94 ARG cc_start: 0.7218 (mmm160) cc_final: 0.4444 (mtt-85) REVERT: U 49 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8445 (mt-10) REVERT: U 83 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: U 97 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8006 (mttp) REVERT: U 143 ARG cc_start: 0.6556 (tpp-160) cc_final: 0.6006 (mtp85) REVERT: U 153 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7506 (mm-30) REVERT: U 211 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: U 308 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8046 (mpt-90) REVERT: W 100 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8906 (mt0) REVERT: X 27 ASP cc_start: 0.7580 (m-30) cc_final: 0.7333 (m-30) REVERT: X 94 ARG cc_start: 0.7095 (mmm160) cc_final: 0.4550 (mtt-85) REVERT: X 103 ARG cc_start: 0.8450 (tpp80) cc_final: 0.8197 (tpp-160) outliers start: 64 outliers final: 30 residues processed: 245 average time/residue: 0.7549 time to fit residues: 204.2034 Evaluate side-chains 233 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 83 GLU Chi-restraints excluded: chain U residue 138 ILE Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 211 GLU Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 308 ARG Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 581 LEU Chi-restraints excluded: chain V residue 612 SER Chi-restraints excluded: chain W residue 100 GLN Chi-restraints excluded: chain X residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 105 optimal weight: 7.9990 chunk 209 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN J 348 GLN J 363 GLN N 31 ASN U 348 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108835 restraints weight = 21992.277| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.04 r_work: 0.3114 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19722 Z= 0.183 Angle : 0.631 9.571 26919 Z= 0.314 Chirality : 0.047 0.331 3225 Planarity : 0.004 0.039 3276 Dihedral : 6.186 58.812 4275 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.62 % Favored : 96.16 % Rotamer: Outliers : 3.29 % Allowed : 11.61 % Favored : 85.10 % 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: 0.35 (0.18), residues: 2268 helix: 1.66 (0.27), residues: 378 sheet: 0.64 (0.20), residues: 705 loop : -0.46 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 143 TYR 0.023 0.002 TYR A 173 PHE 0.015 0.002 PHE M 29 TRP 0.032 0.002 TRP J 479 HIS 0.005 0.001 HIS U 352 Details of bonding type rmsd covalent geometry : bond 0.00442 (19599) covalent geometry : angle 0.60386 (26586) SS BOND : bond 0.00553 ( 36) SS BOND : angle 1.13810 ( 72) hydrogen bonds : bond 0.04865 ( 516) hydrogen bonds : angle 4.45159 ( 1368) link_ALPHA1-3 : bond 0.01071 ( 3) link_ALPHA1-3 : angle 1.19633 ( 9) link_BETA1-4 : bond 0.00381 ( 15) link_BETA1-4 : angle 1.73819 ( 45) link_BETA1-6 : bond 0.00299 ( 6) link_BETA1-6 : angle 1.38783 ( 18) link_NAG-ASN : bond 0.00193 ( 63) link_NAG-ASN : angle 2.00836 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 199 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8416 (mtmt) REVERT: A 142 MET cc_start: 0.6343 (mmm) cc_final: 0.5861 (mmm) REVERT: A 335 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7372 (ttpt) REVERT: A 360 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7113 (ttp80) REVERT: A 412 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6371 (t0) REVERT: B 533 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8822 (mtt) REVERT: B 633 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8203 (mtpt) REVERT: L 94 ARG cc_start: 0.7098 (mmm160) cc_final: 0.4483 (mtt-85) REVERT: L 103 ARG cc_start: 0.8280 (tpp-160) cc_final: 0.8022 (tpp-160) REVERT: J 97 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8065 (mttm) REVERT: J 106 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: J 166 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7776 (mtm110) REVERT: J 246 GLN cc_start: 0.7110 (pt0) cc_final: 0.6428 (pm20) REVERT: K 533 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.8671 (mtp) REVERT: K 626 MET cc_start: 0.8315 (ttp) cc_final: 0.8022 (tpp) REVERT: M 34 MET cc_start: 0.9116 (mtp) cc_final: 0.8750 (mtp) REVERT: N 85 ASP cc_start: 0.8519 (m-30) cc_final: 0.8316 (m-30) REVERT: N 94 ARG cc_start: 0.7118 (mmm160) cc_final: 0.4441 (mtt-85) REVERT: U 49 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8369 (mt-10) REVERT: U 83 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: U 97 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8017 (mttp) REVERT: U 143 ARG cc_start: 0.6559 (tpp-160) cc_final: 0.6034 (mtp85) REVERT: U 153 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7445 (mm-30) REVERT: U 308 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7831 (mpt-90) REVERT: W 100 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8868 (mt0) REVERT: X 27 ASP cc_start: 0.7469 (m-30) cc_final: 0.7249 (m-30) REVERT: X 94 ARG cc_start: 0.7005 (mmm160) cc_final: 0.4552 (mtt-85) REVERT: X 103 ARG cc_start: 0.8429 (tpp80) cc_final: 0.8162 (tpp-160) outliers start: 66 outliers final: 36 residues processed: 246 average time/residue: 0.7334 time to fit residues: 199.2937 Evaluate side-chains 240 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 533 MET Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 83 GLU Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 308 ARG Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 340 GLU Chi-restraints excluded: chain U residue 364 SER Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 581 LEU Chi-restraints excluded: chain V residue 612 SER Chi-restraints excluded: chain W residue 100 GLN Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 24 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 45 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 138 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 129 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN J 348 GLN U 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110529 restraints weight = 22177.675| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.02 r_work: 0.3142 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19722 Z= 0.114 Angle : 0.565 10.359 26919 Z= 0.279 Chirality : 0.044 0.287 3225 Planarity : 0.004 0.038 3276 Dihedral : 5.834 58.147 4275 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.04 % Favored : 96.74 % Rotamer: Outliers : 2.49 % Allowed : 13.05 % Favored : 84.45 % 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: 0.49 (0.18), residues: 2268 helix: 1.84 (0.27), residues: 378 sheet: 0.62 (0.19), residues: 732 loop : -0.34 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 143 TYR 0.024 0.001 TYR A 173 PHE 0.012 0.001 PHE M 29 TRP 0.027 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00262 (19599) covalent geometry : angle 0.53959 (26586) SS BOND : bond 0.00448 ( 36) SS BOND : angle 0.91482 ( 72) hydrogen bonds : bond 0.04005 ( 516) hydrogen bonds : angle 4.30735 ( 1368) link_ALPHA1-3 : bond 0.01072 ( 3) link_ALPHA1-3 : angle 1.17483 ( 9) link_BETA1-4 : bond 0.00378 ( 15) link_BETA1-4 : angle 1.60156 ( 45) link_BETA1-6 : bond 0.00385 ( 6) link_BETA1-6 : angle 1.23142 ( 18) link_NAG-ASN : bond 0.00198 ( 63) link_NAG-ASN : angle 1.82425 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 203 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8052 (mmtt) REVERT: A 142 MET cc_start: 0.6375 (mmm) cc_final: 0.5892 (mmm) REVERT: A 360 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7164 (ttp80) REVERT: A 412 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6608 (t0) REVERT: A 475 MET cc_start: 0.8419 (mmt) cc_final: 0.7496 (mmt) REVERT: B 533 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8823 (mtt) REVERT: L 94 ARG cc_start: 0.7064 (mmm160) cc_final: 0.4518 (mtt-85) REVERT: L 103 ARG cc_start: 0.8280 (tpp-160) cc_final: 0.8004 (tpp-160) REVERT: J 97 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8084 (mttt) REVERT: J 166 ARG cc_start: 0.8003 (mtp-110) cc_final: 0.7780 (mtm110) REVERT: J 208 VAL cc_start: 0.6389 (t) cc_final: 0.6087 (p) REVERT: J 246 GLN cc_start: 0.7014 (pt0) cc_final: 0.6392 (pm20) REVERT: K 533 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8618 (mtp) REVERT: K 626 MET cc_start: 0.8123 (ttp) cc_final: 0.7858 (tpp) REVERT: M 34 MET cc_start: 0.9107 (mtp) cc_final: 0.8731 (mtp) REVERT: N 94 ARG cc_start: 0.7154 (mmm160) cc_final: 0.4507 (mtt-85) REVERT: U 49 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8368 (mt-10) REVERT: U 83 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: U 97 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8024 (mttp) REVERT: U 143 ARG cc_start: 0.6550 (tpp-160) cc_final: 0.6016 (mtp85) REVERT: U 153 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7421 (mm-30) REVERT: U 231 LYS cc_start: 0.8470 (mmtm) cc_final: 0.7967 (mppt) REVERT: U 308 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7841 (mpt-90) REVERT: W 100 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8790 (mt0) REVERT: X 94 ARG cc_start: 0.6926 (mmm160) cc_final: 0.4516 (mtt-85) REVERT: X 103 ARG cc_start: 0.8422 (tpp80) cc_final: 0.8153 (tpp-160) outliers start: 50 outliers final: 27 residues processed: 235 average time/residue: 0.7516 time to fit residues: 195.3856 Evaluate side-chains 231 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 533 MET Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain U residue 83 GLU Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 308 ARG Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain W residue 100 GLN Chi-restraints excluded: chain X residue 24 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 161 optimal weight: 3.9990 chunk 93 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 164 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN J 348 GLN N 31 ASN U 258 GLN U 348 GLN U 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112712 restraints weight = 22173.617| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.02 r_work: 0.3186 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19722 Z= 0.097 Angle : 0.533 11.015 26919 Z= 0.263 Chirality : 0.043 0.253 3225 Planarity : 0.004 0.036 3276 Dihedral : 5.462 57.286 4275 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 2.14 % Allowed : 13.15 % Favored : 84.70 % 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: 0.67 (0.18), residues: 2268 helix: 2.40 (0.27), residues: 360 sheet: 0.68 (0.20), residues: 735 loop : -0.30 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 143 TYR 0.024 0.001 TYR A 173 PHE 0.009 0.001 PHE M 29 TRP 0.028 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00217 (19599) covalent geometry : angle 0.51183 (26586) SS BOND : bond 0.00399 ( 36) SS BOND : angle 0.80623 ( 72) hydrogen bonds : bond 0.03558 ( 516) hydrogen bonds : angle 4.15083 ( 1368) link_ALPHA1-3 : bond 0.00962 ( 3) link_ALPHA1-3 : angle 1.17832 ( 9) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 1.47946 ( 45) link_BETA1-6 : bond 0.00420 ( 6) link_BETA1-6 : angle 1.16381 ( 18) link_NAG-ASN : bond 0.00220 ( 63) link_NAG-ASN : angle 1.64405 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8247 (mttp) REVERT: A 142 MET cc_start: 0.6369 (mmm) cc_final: 0.5875 (mmm) REVERT: A 173 TYR cc_start: 0.7719 (p90) cc_final: 0.7360 (p90) REVERT: A 246 GLN cc_start: 0.6806 (pm20) cc_final: 0.6553 (pt0) REVERT: A 360 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7161 (ttp80) REVERT: B 533 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8801 (mtt) REVERT: L 94 ARG cc_start: 0.7036 (mmm160) cc_final: 0.4455 (mtt-85) REVERT: L 103 ARG cc_start: 0.8253 (tpp-160) cc_final: 0.7969 (tpp-160) REVERT: J 97 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7972 (mttt) REVERT: J 166 ARG cc_start: 0.8043 (mtp-110) cc_final: 0.7750 (mtm110) REVERT: J 246 GLN cc_start: 0.6926 (pt0) cc_final: 0.6268 (pm20) REVERT: K 533 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8596 (mtp) REVERT: M 34 MET cc_start: 0.9087 (mtp) cc_final: 0.8698 (mtp) REVERT: N 94 ARG cc_start: 0.7182 (mmm160) cc_final: 0.4583 (mtt-85) REVERT: U 49 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8328 (mt-10) REVERT: U 97 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7977 (mttp) REVERT: U 143 ARG cc_start: 0.6623 (tpp-160) cc_final: 0.6151 (mtp85) REVERT: U 153 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7380 (mm-30) REVERT: U 308 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7804 (mpt-90) REVERT: X 94 ARG cc_start: 0.6922 (mmm160) cc_final: 0.4568 (mtt-85) REVERT: X 103 ARG cc_start: 0.8390 (tpp80) cc_final: 0.8086 (tpp-160) outliers start: 43 outliers final: 22 residues processed: 236 average time/residue: 0.7212 time to fit residues: 188.5688 Evaluate side-chains 225 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 533 MET Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 308 ARG Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 164 optimal weight: 0.0870 chunk 139 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 160 optimal weight: 0.0010 chunk 119 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 348 GLN J 348 GLN U 348 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112759 restraints weight = 22095.017| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.01 r_work: 0.3188 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19722 Z= 0.100 Angle : 0.536 10.971 26919 Z= 0.264 Chirality : 0.043 0.252 3225 Planarity : 0.004 0.037 3276 Dihedral : 5.328 56.573 4275 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.22 % Favored : 96.65 % Rotamer: Outliers : 1.74 % Allowed : 14.05 % Favored : 84.21 % 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: 0.71 (0.18), residues: 2268 helix: 2.39 (0.27), residues: 360 sheet: 0.71 (0.20), residues: 735 loop : -0.25 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 143 TYR 0.025 0.001 TYR U 173 PHE 0.010 0.001 PHE M 29 TRP 0.027 0.001 TRP J 479 HIS 0.003 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00226 (19599) covalent geometry : angle 0.51577 (26586) SS BOND : bond 0.00401 ( 36) SS BOND : angle 0.81814 ( 72) hydrogen bonds : bond 0.03648 ( 516) hydrogen bonds : angle 4.14411 ( 1368) link_ALPHA1-3 : bond 0.00907 ( 3) link_ALPHA1-3 : angle 1.21428 ( 9) link_BETA1-4 : bond 0.00368 ( 15) link_BETA1-4 : angle 1.44732 ( 45) link_BETA1-6 : bond 0.00392 ( 6) link_BETA1-6 : angle 1.21070 ( 18) link_NAG-ASN : bond 0.00187 ( 63) link_NAG-ASN : angle 1.60656 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8170 (mttp) REVERT: A 142 MET cc_start: 0.6337 (mmm) cc_final: 0.5851 (mmm) REVERT: A 173 TYR cc_start: 0.7702 (p90) cc_final: 0.7333 (p90) REVERT: A 360 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7171 (ttp80) REVERT: A 375 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 533 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8798 (mtt) REVERT: L 31 ASN cc_start: 0.8611 (m110) cc_final: 0.8377 (m-40) REVERT: L 94 ARG cc_start: 0.7042 (mmm160) cc_final: 0.4501 (mtt-85) REVERT: L 103 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7958 (tpp-160) REVERT: J 97 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7979 (mttt) REVERT: J 166 ARG cc_start: 0.8056 (mtp-110) cc_final: 0.7765 (mtm110) REVERT: J 208 VAL cc_start: 0.6408 (t) cc_final: 0.6089 (p) REVERT: J 246 GLN cc_start: 0.6881 (pt0) cc_final: 0.6259 (pm20) REVERT: K 533 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8542 (mtp) REVERT: N 94 ARG cc_start: 0.7159 (mmm160) cc_final: 0.4568 (mtt-85) REVERT: U 49 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8315 (mt-10) REVERT: U 97 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7922 (mttt) REVERT: U 143 ARG cc_start: 0.6466 (tpp-160) cc_final: 0.5974 (mtp85) REVERT: U 153 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7374 (mm-30) REVERT: U 308 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7755 (mpt-90) REVERT: U 412 ASP cc_start: 0.6694 (OUTLIER) cc_final: 0.6487 (t0) REVERT: X 94 ARG cc_start: 0.6924 (mmm160) cc_final: 0.4562 (mtt-85) REVERT: X 103 ARG cc_start: 0.8413 (tpp80) cc_final: 0.8110 (tpp-160) outliers start: 35 outliers final: 18 residues processed: 229 average time/residue: 0.7377 time to fit residues: 186.9958 Evaluate side-chains 224 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 533 MET Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 308 ARG Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 156 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 348 GLN J 348 GLN U 348 GLN U 363 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.148007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109291 restraints weight = 22076.824| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.03 r_work: 0.3129 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19722 Z= 0.176 Angle : 0.621 11.964 26919 Z= 0.307 Chirality : 0.047 0.468 3225 Planarity : 0.004 0.038 3276 Dihedral : 5.615 56.554 4275 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 1.84 % Allowed : 13.95 % Favored : 84.21 % 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: 0.51 (0.18), residues: 2268 helix: 1.74 (0.27), residues: 378 sheet: 0.74 (0.20), residues: 699 loop : -0.34 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 143 TYR 0.024 0.002 TYR U 173 PHE 0.014 0.002 PHE M 29 TRP 0.032 0.002 TRP J 479 HIS 0.004 0.001 HIS J 352 Details of bonding type rmsd covalent geometry : bond 0.00423 (19599) covalent geometry : angle 0.59708 (26586) SS BOND : bond 0.00524 ( 36) SS BOND : angle 1.06576 ( 72) hydrogen bonds : bond 0.04675 ( 516) hydrogen bonds : angle 4.30876 ( 1368) link_ALPHA1-3 : bond 0.00836 ( 3) link_ALPHA1-3 : angle 1.27138 ( 9) link_BETA1-4 : bond 0.00350 ( 15) link_BETA1-4 : angle 1.53888 ( 45) link_BETA1-6 : bond 0.00268 ( 6) link_BETA1-6 : angle 1.38414 ( 18) link_NAG-ASN : bond 0.00201 ( 63) link_NAG-ASN : angle 1.85436 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6396 (mmm) cc_final: 0.5930 (mmm) REVERT: A 173 TYR cc_start: 0.7738 (p90) cc_final: 0.7357 (p90) REVERT: A 360 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7157 (ttp80) REVERT: B 533 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8846 (mtt) REVERT: L 31 ASN cc_start: 0.8755 (m110) cc_final: 0.8543 (m-40) REVERT: L 94 ARG cc_start: 0.6959 (mmm160) cc_final: 0.4464 (mtt-85) REVERT: J 97 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8006 (mttp) REVERT: J 166 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7798 (mtm110) REVERT: J 208 VAL cc_start: 0.6396 (t) cc_final: 0.6089 (p) REVERT: J 246 GLN cc_start: 0.7032 (pt0) cc_final: 0.6392 (pm20) REVERT: K 533 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.8638 (mtp) REVERT: M 34 MET cc_start: 0.9118 (mtp) cc_final: 0.8712 (mtp) REVERT: N 94 ARG cc_start: 0.7186 (mmm160) cc_final: 0.4471 (mtt-85) REVERT: U 49 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8357 (mt-10) REVERT: U 97 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8008 (mttt) REVERT: U 143 ARG cc_start: 0.6476 (tpp-160) cc_final: 0.6032 (mtp85) REVERT: U 153 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7400 (mm-30) REVERT: U 308 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7879 (mpt-90) REVERT: X 94 ARG cc_start: 0.7009 (mmm160) cc_final: 0.4533 (mtt-85) REVERT: X 103 ARG cc_start: 0.8445 (tpp80) cc_final: 0.8145 (tpp-160) outliers start: 37 outliers final: 24 residues processed: 226 average time/residue: 0.7204 time to fit residues: 180.0396 Evaluate side-chains 223 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 533 MET Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain K residue 639 THR Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 308 ARG Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 129 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 202 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 348 GLN J 348 GLN U 348 GLN X 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110474 restraints weight = 22145.567| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.03 r_work: 0.3147 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19722 Z= 0.127 Angle : 0.582 11.989 26919 Z= 0.287 Chirality : 0.045 0.425 3225 Planarity : 0.004 0.036 3276 Dihedral : 5.545 57.188 4275 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 1.89 % Allowed : 13.95 % Favored : 84.16 % 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: 0.48 (0.18), residues: 2268 helix: 1.79 (0.27), residues: 378 sheet: 0.66 (0.20), residues: 717 loop : -0.36 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 143 TYR 0.026 0.001 TYR U 173 PHE 0.013 0.001 PHE M 29 TRP 0.030 0.001 TRP J 479 HIS 0.003 0.001 HIS J 352 Details of bonding type rmsd covalent geometry : bond 0.00298 (19599) covalent geometry : angle 0.55821 (26586) SS BOND : bond 0.00464 ( 36) SS BOND : angle 0.97523 ( 72) hydrogen bonds : bond 0.04155 ( 516) hydrogen bonds : angle 4.26911 ( 1368) link_ALPHA1-3 : bond 0.00887 ( 3) link_ALPHA1-3 : angle 1.26315 ( 9) link_BETA1-4 : bond 0.00338 ( 15) link_BETA1-4 : angle 1.49310 ( 45) link_BETA1-6 : bond 0.00326 ( 6) link_BETA1-6 : angle 1.27582 ( 18) link_NAG-ASN : bond 0.00193 ( 63) link_NAG-ASN : angle 1.79247 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7571.13 seconds wall clock time: 129 minutes 39.85 seconds (7779.85 seconds total)