Starting phenix.real_space_refine on Tue Jun 17 02:17:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t75_25734/06_2025/7t75_25734.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t75_25734/06_2025/7t75_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t75_25734/06_2025/7t75_25734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t75_25734/06_2025/7t75_25734.map" model { file = "/net/cci-nas-00/data/ceres_data/7t75_25734/06_2025/7t75_25734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t75_25734/06_2025/7t75_25734.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.28, per 1000 atoms: 0.64 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: 5.41 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.24 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: 6.44 Time building geometry restraints manager: 6.17 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: 5.060 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: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 45.390 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.120 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:14.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (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 TRP 0.050 0.009 TRP J 96 HIS 0.012 0.003 HIS J 85 PHE 0.040 0.007 PHE A 353 TYR 0.064 0.008 TYR L 96 ARG 0.014 0.001 ARG M 71 Details of bonding type rmsd link_NAG-ASN : bond 0.06887 ( 63) link_NAG-ASN : angle 2.69601 ( 189) link_BETA1-4 : bond 0.07157 ( 15) link_BETA1-4 : angle 4.76798 ( 45) link_ALPHA1-3 : bond 0.07667 ( 3) link_ALPHA1-3 : angle 3.97063 ( 9) hydrogen bonds : bond 0.17588 ( 516) hydrogen bonds : angle 6.64987 ( 1368) link_BETA1-6 : bond 0.05219 ( 6) link_BETA1-6 : angle 2.60889 ( 18) SS BOND : bond 0.01349 ( 36) SS BOND : angle 3.28449 ( 72) covalent geometry : bond 0.02209 (19599) covalent geometry : angle 1.82657 (26586) *********************** 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 : 2.232 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: 0.5553 (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: 0.6542 (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: 1.6247 time to fit residues: 762.3620 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 : 2.207 ------------------------------------------------------------------------------- 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 189 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.151498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112048 restraints weight = 22228.336| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.17 r_work: 0.3174 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2270 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= 0.148 Angle : 0.705 10.986 26919 Z= 0.349 Chirality : 0.047 0.255 3225 Planarity : 0.004 0.053 3276 Dihedral : 8.778 76.580 4277 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.43 % Favored : 97.18 % Rotamer: Outliers : 3.19 % Allowed : 9.52 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2268 helix: 1.24 (0.27), residues: 375 sheet: 0.71 (0.19), residues: 708 loop : 0.04 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 479 HIS 0.004 0.001 HIS J 85 PHE 0.016 0.002 PHE A 176 TYR 0.011 0.001 TYR X 96 ARG 0.006 0.001 ARG A 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 63) link_NAG-ASN : angle 2.98291 ( 189) link_BETA1-4 : bond 0.00598 ( 15) link_BETA1-4 : angle 2.59031 ( 45) link_ALPHA1-3 : bond 0.01518 ( 3) link_ALPHA1-3 : angle 2.19446 ( 9) hydrogen bonds : bond 0.05093 ( 516) hydrogen bonds : angle 4.83607 ( 1368) link_BETA1-6 : bond 0.00690 ( 6) link_BETA1-6 : angle 1.00654 ( 18) SS BOND : bond 0.00206 ( 36) SS BOND : angle 1.44605 ( 72) covalent geometry : bond 0.00328 (19599) covalent geometry : angle 0.64901 (26586) *********************** 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 315 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 251 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8953 (mtp) cc_final: 0.8696 (mtp) REVERT: A 142 MET cc_start: 0.6323 (mmm) cc_final: 0.5678 (mmm) REVERT: L 94 ARG cc_start: 0.7291 (mmm160) cc_final: 0.4812 (mtt180) REVERT: J 97 LYS cc_start: 0.8387 (mmtt) cc_final: 0.7951 (mttt) REVERT: J 166 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7701 (mtm110) REVERT: J 348 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7567 (mp-120) REVERT: M 23 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6676 (tmt170) REVERT: N 94 ARG cc_start: 0.7191 (mmm160) cc_final: 0.4699 (mtt-85) REVERT: U 83 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: U 97 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7985 (mttp) REVERT: U 102 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7630 (mp0) REVERT: U 106 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: U 142 MET cc_start: 0.6648 (mmm) cc_final: 0.6340 (mmm) REVERT: U 143 ARG cc_start: 0.6546 (tpp-160) cc_final: 0.5969 (mtp85) REVERT: U 153 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7539 (mm-30) REVERT: U 348 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.6640 (mp-120) REVERT: W 23 ARG cc_start: 0.8326 (tmt170) cc_final: 0.8033 (tmt170) REVERT: W 100 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8328 (p) REVERT: X 94 ARG cc_start: 0.7168 (mmm160) cc_final: 0.4706 (mtt-85) REVERT: X 103 ARG cc_start: 0.7668 (tpp-160) cc_final: 0.7438 (tpp-160) outliers start: 64 outliers final: 30 residues processed: 298 average time/residue: 2.1729 time to fit residues: 719.7965 Evaluate side-chains 239 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 3.113 ------------------------------------------------------------------------------- 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 J residue 348 GLN 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 190 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 217 optimal weight: 0.1980 chunk 67 optimal weight: 0.0060 chunk 218 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 258 GLN J 283 ASN 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 = 0.3774 r_free = 0.3774 target = 0.152693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114780 restraints weight = 22183.889| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.02 r_work: 0.3223 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19722 Z= 0.115 Angle : 0.589 9.424 26919 Z= 0.293 Chirality : 0.045 0.270 3225 Planarity : 0.004 0.045 3276 Dihedral : 7.300 59.948 4277 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.00 % Favored : 96.78 % Rotamer: Outliers : 2.94 % Allowed : 10.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2268 helix: 2.12 (0.27), residues: 357 sheet: 0.65 (0.19), residues: 717 loop : -0.12 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 PHE 0.011 0.002 PHE A 176 TYR 0.019 0.001 TYR A 173 ARG 0.008 0.000 ARG J 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 63) link_NAG-ASN : angle 2.10652 ( 189) link_BETA1-4 : bond 0.00617 ( 15) link_BETA1-4 : angle 1.92672 ( 45) link_ALPHA1-3 : bond 0.01305 ( 3) link_ALPHA1-3 : angle 1.10390 ( 9) hydrogen bonds : bond 0.04096 ( 516) hydrogen bonds : angle 4.39631 ( 1368) link_BETA1-6 : bond 0.00485 ( 6) link_BETA1-6 : angle 1.15852 ( 18) SS BOND : bond 0.00632 ( 36) SS BOND : angle 1.08115 ( 72) covalent geometry : bond 0.00252 (19599) covalent geometry : angle 0.55550 (26586) *********************** 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: 59 poor density : 221 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6436 (mmm) cc_final: 0.5939 (mmm) REVERT: A 208 VAL cc_start: 0.6512 (t) cc_final: 0.6220 (p) REVERT: A 412 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6841 (t0) REVERT: A 428 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6345 (mt0) REVERT: B 533 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8718 (mtt) REVERT: L 94 ARG cc_start: 0.7169 (mmm160) cc_final: 0.4668 (mtt-85) REVERT: J 97 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7846 (mttt) REVERT: J 106 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: J 166 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7481 (mtm110) REVERT: J 208 VAL cc_start: 0.6568 (t) cc_final: 0.6296 (p) REVERT: K 616 ASN cc_start: 0.8384 (p0) cc_final: 0.7951 (t0) REVERT: M 23 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.6619 (tmt170) REVERT: M 52 ASN cc_start: 0.7508 (t0) cc_final: 0.7305 (t0) REVERT: N 94 ARG cc_start: 0.7100 (mmm160) cc_final: 0.4554 (mtt-85) REVERT: U 97 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7869 (mttp) REVERT: U 142 MET cc_start: 0.6637 (mmm) cc_final: 0.6258 (mmm) REVERT: U 143 ARG cc_start: 0.6437 (tpp-160) cc_final: 0.5954 (mtp85) REVERT: U 153 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7441 (mm-30) REVERT: W 100 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8264 (p) REVERT: X 94 ARG cc_start: 0.7097 (mmm160) cc_final: 0.4687 (mtt180) outliers start: 59 outliers final: 26 residues processed: 262 average time/residue: 1.5228 time to fit residues: 445.7943 Evaluate side-chains 226 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 2.650 ------------------------------------------------------------------------------- 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 141 ASP 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 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 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 595 ILE 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 V residue 536 THR Chi-restraints excluded: chain W residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 348 GLN X 31 ASN X 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110838 restraints weight = 22295.523| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.04 r_work: 0.3168 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19722 Z= 0.157 Angle : 0.616 9.680 26919 Z= 0.306 Chirality : 0.046 0.267 3225 Planarity : 0.004 0.035 3276 Dihedral : 6.433 59.561 4277 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.95 % Favored : 96.83 % Rotamer: Outliers : 3.54 % Allowed : 10.61 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2268 helix: 1.79 (0.27), residues: 378 sheet: 0.66 (0.19), residues: 717 loop : -0.25 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 479 HIS 0.004 0.001 HIS U 352 PHE 0.017 0.002 PHE M 29 TYR 0.020 0.001 TYR A 173 ARG 0.004 0.000 ARG J 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 63) link_NAG-ASN : angle 1.95626 ( 189) link_BETA1-4 : bond 0.00515 ( 15) link_BETA1-4 : angle 1.90792 ( 45) link_ALPHA1-3 : bond 0.01285 ( 3) link_ALPHA1-3 : angle 1.32712 ( 9) hydrogen bonds : bond 0.04600 ( 516) hydrogen bonds : angle 4.37155 ( 1368) link_BETA1-6 : bond 0.00334 ( 6) link_BETA1-6 : angle 1.27884 ( 18) SS BOND : bond 0.00537 ( 36) SS BOND : angle 1.15895 ( 72) covalent geometry : bond 0.00372 (19599) covalent geometry : angle 0.58754 (26586) *********************** 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 274 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 203 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8204 (mtmt) REVERT: A 142 MET cc_start: 0.6401 (mmm) cc_final: 0.5962 (mmm) REVERT: A 208 VAL cc_start: 0.6509 (t) cc_final: 0.6206 (p) REVERT: A 335 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7325 (ttpt) REVERT: A 412 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6447 (t0) REVERT: A 428 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6532 (mt0) REVERT: B 533 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8755 (mtt) REVERT: B 633 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8161 (mtpt) REVERT: L 94 ARG cc_start: 0.7122 (mmm160) cc_final: 0.4529 (mtt-85) REVERT: J 97 LYS cc_start: 0.8365 (mmtt) cc_final: 0.7836 (mttp) REVERT: J 166 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7537 (mtm110) REVERT: J 208 VAL cc_start: 0.6490 (t) cc_final: 0.6202 (p) REVERT: M 23 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6609 (tmt170) REVERT: N 85 ASP cc_start: 0.8477 (m-30) cc_final: 0.8256 (m-30) REVERT: N 94 ARG cc_start: 0.6950 (mmm160) cc_final: 0.4388 (mtt-85) REVERT: N 103 ARG cc_start: 0.8226 (tpp80) cc_final: 0.8013 (tpp-160) REVERT: U 97 LYS cc_start: 0.8358 (mmtt) cc_final: 0.7914 (mttp) REVERT: U 142 MET cc_start: 0.6583 (mmm) cc_final: 0.6175 (mmm) REVERT: U 143 ARG cc_start: 0.6357 (tpp-160) cc_final: 0.5813 (mtp85) REVERT: U 153 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7426 (mm-30) REVERT: U 348 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.6364 (mp-120) REVERT: W 100 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8556 (p) REVERT: X 27 ASP cc_start: 0.7457 (m-30) cc_final: 0.7197 (m-30) REVERT: X 94 ARG cc_start: 0.7066 (mmm160) cc_final: 0.4559 (mtt180) REVERT: X 103 ARG cc_start: 0.8302 (tpp80) cc_final: 0.8072 (tpp-160) outliers start: 71 outliers final: 37 residues processed: 254 average time/residue: 1.4719 time to fit residues: 415.6989 Evaluate side-chains 237 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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 125 LEU 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 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 348 GLN Chi-restraints excluded: chain U residue 364 SER Chi-restraints excluded: chain U residue 371 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 Chi-restraints excluded: chain W residue 100 SER 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 202 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 140 optimal weight: 0.0170 chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 219 optimal weight: 0.0870 chunk 200 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- 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 363 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 = 0.3734 r_free = 0.3734 target = 0.149253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111065 restraints weight = 22339.520| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.07 r_work: 0.3145 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19722 Z= 0.142 Angle : 0.592 10.258 26919 Z= 0.293 Chirality : 0.045 0.261 3225 Planarity : 0.004 0.035 3276 Dihedral : 6.063 59.330 4277 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.69 % Favored : 97.09 % Rotamer: Outliers : 3.14 % Allowed : 11.86 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2268 helix: 1.85 (0.27), residues: 378 sheet: 0.65 (0.19), residues: 735 loop : -0.25 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 PHE 0.014 0.002 PHE M 29 TYR 0.021 0.001 TYR A 173 ARG 0.007 0.000 ARG J 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 63) link_NAG-ASN : angle 1.94460 ( 189) link_BETA1-4 : bond 0.00479 ( 15) link_BETA1-4 : angle 1.76897 ( 45) link_ALPHA1-3 : bond 0.01184 ( 3) link_ALPHA1-3 : angle 1.13360 ( 9) hydrogen bonds : bond 0.04384 ( 516) hydrogen bonds : angle 4.32889 ( 1368) link_BETA1-6 : bond 0.00352 ( 6) link_BETA1-6 : angle 1.26780 ( 18) SS BOND : bond 0.00503 ( 36) SS BOND : angle 1.03571 ( 72) covalent geometry : bond 0.00335 (19599) covalent geometry : angle 0.56460 (26586) *********************** 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 266 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6441 (mmm) cc_final: 0.6011 (mmm) REVERT: A 208 VAL cc_start: 0.6530 (t) cc_final: 0.6233 (p) REVERT: A 412 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6838 (t0) REVERT: A 428 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6624 (mt0) REVERT: B 533 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8780 (mtt) REVERT: L 94 ARG cc_start: 0.7159 (mmm160) cc_final: 0.4651 (mtt180) REVERT: J 97 LYS cc_start: 0.8404 (mmtt) cc_final: 0.7947 (mttt) REVERT: J 166 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7682 (mtm110) REVERT: J 208 VAL cc_start: 0.6494 (t) cc_final: 0.6203 (p) REVERT: J 348 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7646 (mp-120) REVERT: N 94 ARG cc_start: 0.6974 (mmm160) cc_final: 0.4419 (mtt-85) REVERT: N 103 ARG cc_start: 0.8257 (tpp80) cc_final: 0.8015 (tpp-160) REVERT: U 83 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: U 97 LYS cc_start: 0.8400 (mmtt) cc_final: 0.7939 (mttp) REVERT: U 142 MET cc_start: 0.6746 (mmm) cc_final: 0.6255 (mmm) REVERT: U 143 ARG cc_start: 0.6326 (tpp-160) cc_final: 0.5775 (mtp85) REVERT: U 153 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7449 (mm-30) REVERT: W 100 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8644 (p) REVERT: X 27 ASP cc_start: 0.7421 (m-30) cc_final: 0.7184 (m-30) REVERT: X 94 ARG cc_start: 0.7044 (mmm160) cc_final: 0.4553 (mtt-85) REVERT: X 103 ARG cc_start: 0.8345 (tpp80) cc_final: 0.8100 (tpp-160) outliers start: 63 outliers final: 35 residues processed: 243 average time/residue: 1.4818 time to fit residues: 400.0002 Evaluate side-chains 235 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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 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 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 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 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 348 GLN Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain M residue 5 VAL 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 213 ILE 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 SER 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 103 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 156 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 168 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 U 348 GLN X 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111687 restraints weight = 22267.096| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.03 r_work: 0.3165 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3189 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 : 0.556 10.487 26919 Z= 0.275 Chirality : 0.044 0.259 3225 Planarity : 0.004 0.033 3276 Dihedral : 5.788 59.154 4277 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.87 % Favored : 96.91 % Rotamer: Outliers : 2.79 % Allowed : 12.46 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2268 helix: 2.32 (0.27), residues: 360 sheet: 0.62 (0.19), residues: 735 loop : -0.26 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 PHE 0.011 0.001 PHE M 29 TYR 0.024 0.001 TYR U 173 ARG 0.008 0.000 ARG J 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 63) link_NAG-ASN : angle 1.77056 ( 189) link_BETA1-4 : bond 0.00438 ( 15) link_BETA1-4 : angle 1.65777 ( 45) link_ALPHA1-3 : bond 0.01182 ( 3) link_ALPHA1-3 : angle 1.15546 ( 9) hydrogen bonds : bond 0.03979 ( 516) hydrogen bonds : angle 4.23735 ( 1368) link_BETA1-6 : bond 0.00389 ( 6) link_BETA1-6 : angle 1.22018 ( 18) SS BOND : bond 0.00443 ( 36) SS BOND : angle 0.90564 ( 72) covalent geometry : bond 0.00260 (19599) covalent geometry : angle 0.53129 (26586) *********************** 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 262 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6434 (mmm) cc_final: 0.6017 (mmm) REVERT: A 375 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 412 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6425 (t0) REVERT: A 428 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6605 (mt0) REVERT: A 475 MET cc_start: 0.8427 (mmt) cc_final: 0.8182 (mmt) REVERT: B 533 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8789 (mtt) REVERT: L 94 ARG cc_start: 0.7146 (mmm160) cc_final: 0.4642 (mtt-85) REVERT: J 97 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7935 (mttt) REVERT: J 106 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: J 166 ARG cc_start: 0.7930 (mtp-110) cc_final: 0.7666 (mtm110) REVERT: J 208 VAL cc_start: 0.6507 (t) cc_final: 0.6211 (p) REVERT: J 246 GLN cc_start: 0.7031 (pt0) cc_final: 0.6366 (pm20) REVERT: K 575 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6621 (tt0) REVERT: N 94 ARG cc_start: 0.6929 (mmm160) cc_final: 0.4505 (mtt-85) REVERT: N 103 ARG cc_start: 0.8308 (tpp80) cc_final: 0.8044 (tpp-160) REVERT: U 97 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7979 (mttp) REVERT: U 143 ARG cc_start: 0.6354 (tpp-160) cc_final: 0.5798 (mtp85) REVERT: U 153 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7443 (mm-30) REVERT: U 308 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7828 (mpt-90) REVERT: W 100 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8746 (mt0) REVERT: X 27 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: X 94 ARG cc_start: 0.7094 (mmm160) cc_final: 0.4567 (mtt-85) REVERT: X 103 ARG cc_start: 0.8338 (tpp80) cc_final: 0.8087 (tpp-160) outliers start: 56 outliers final: 26 residues processed: 243 average time/residue: 1.4557 time to fit residues: 394.2358 Evaluate side-chains 228 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 141 ASP 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 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 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 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 575 GLN Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain U residue 46 LYS 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 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 27 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 88 optimal weight: 0.0370 chunk 43 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- 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 M 52 ASN U 348 GLN X 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115286 restraints weight = 21957.759| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.71 r_work: 0.3029 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 19722 Z= 0.238 Angle : 0.691 11.009 26919 Z= 0.342 Chirality : 0.048 0.260 3225 Planarity : 0.005 0.036 3276 Dihedral : 6.173 58.966 4275 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.62 % Favored : 96.16 % Rotamer: Outliers : 2.99 % Allowed : 12.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2268 helix: 1.62 (0.27), residues: 378 sheet: 0.61 (0.20), residues: 708 loop : -0.46 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 479 HIS 0.006 0.002 HIS U 352 PHE 0.018 0.003 PHE M 29 TYR 0.021 0.002 TYR U 173 ARG 0.008 0.001 ARG J 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 63) link_NAG-ASN : angle 1.99548 ( 189) link_BETA1-4 : bond 0.00418 ( 15) link_BETA1-4 : angle 1.81851 ( 45) link_ALPHA1-3 : bond 0.01200 ( 3) link_ALPHA1-3 : angle 1.26670 ( 9) hydrogen bonds : bond 0.05498 ( 516) hydrogen bonds : angle 4.48565 ( 1368) link_BETA1-6 : bond 0.00250 ( 6) link_BETA1-6 : angle 1.50926 ( 18) SS BOND : bond 0.00605 ( 36) SS BOND : angle 1.28924 ( 72) covalent geometry : bond 0.00581 (19599) covalent geometry : angle 0.66516 (26586) *********************** 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 256 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: A 142 MET cc_start: 0.6390 (mmm) cc_final: 0.5909 (mmm) REVERT: A 428 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6874 (mt0) REVERT: A 475 MET cc_start: 0.8606 (mmt) cc_final: 0.7730 (mmt) REVERT: B 533 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8906 (mtp) REVERT: B 633 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8277 (mtpt) REVERT: L 94 ARG cc_start: 0.7256 (mmm160) cc_final: 0.4665 (mtt-85) REVERT: L 103 ARG cc_start: 0.8324 (tpp-160) cc_final: 0.8085 (tpp-160) REVERT: J 97 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8220 (mttp) REVERT: J 166 ARG cc_start: 0.8153 (mtp-110) cc_final: 0.7847 (mtm110) REVERT: J 246 GLN cc_start: 0.7220 (pt0) cc_final: 0.6511 (pm20) REVERT: K 533 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.8886 (mtp) REVERT: M 52 ASN cc_start: 0.8299 (t0) cc_final: 0.7788 (t0) REVERT: N 94 ARG cc_start: 0.7274 (mmm160) cc_final: 0.4483 (mtt-85) REVERT: U 83 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: U 97 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8094 (mttp) REVERT: U 143 ARG cc_start: 0.6414 (tpp-160) cc_final: 0.5827 (mtp85) REVERT: U 153 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7528 (mm-30) REVERT: U 211 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: U 308 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7953 (mpt-90) REVERT: W 100 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8907 (mt0) REVERT: X 27 ASP cc_start: 0.7570 (m-30) cc_final: 0.7330 (m-30) REVERT: X 94 ARG cc_start: 0.7090 (mmm160) cc_final: 0.4498 (mtt-85) REVERT: X 103 ARG cc_start: 0.8483 (tpp80) cc_final: 0.8223 (tpp-160) outliers start: 60 outliers final: 33 residues processed: 237 average time/residue: 1.4919 time to fit residues: 395.5171 Evaluate side-chains 230 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU 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 290 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 375 SER 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 633 LYS 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 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 533 MET 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 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 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 139 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 183 optimal weight: 0.7980 chunk 175 optimal weight: 0.3980 chunk 178 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 77 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 N 31 ASN U 258 GLN U 348 GLN U 377 ASN X 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111754 restraints weight = 22246.403| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.03 r_work: 0.3159 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19722 Z= 0.106 Angle : 0.554 10.919 26919 Z= 0.273 Chirality : 0.044 0.280 3225 Planarity : 0.004 0.038 3276 Dihedral : 5.756 58.142 4275 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.00 % Favored : 96.87 % Rotamer: Outliers : 2.04 % Allowed : 13.70 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2268 helix: 2.24 (0.27), residues: 360 sheet: 0.56 (0.19), residues: 732 loop : -0.32 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 PHE 0.010 0.001 PHE M 29 TYR 0.026 0.001 TYR A 173 ARG 0.007 0.000 ARG J 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 63) link_NAG-ASN : angle 1.84713 ( 189) link_BETA1-4 : bond 0.00387 ( 15) link_BETA1-4 : angle 1.57052 ( 45) link_ALPHA1-3 : bond 0.01047 ( 3) link_ALPHA1-3 : angle 1.16474 ( 9) hydrogen bonds : bond 0.03819 ( 516) hydrogen bonds : angle 4.24947 ( 1368) link_BETA1-6 : bond 0.00442 ( 6) link_BETA1-6 : angle 1.16986 ( 18) SS BOND : bond 0.00422 ( 36) SS BOND : angle 0.86248 ( 72) covalent geometry : bond 0.00239 (19599) covalent geometry : angle 0.52846 (26586) *********************** 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 243 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6386 (mmm) cc_final: 0.5897 (mmm) REVERT: A 375 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8679 (p) REVERT: A 475 MET cc_start: 0.8444 (mmt) cc_final: 0.7542 (mmt) REVERT: B 533 MET cc_start: 0.9137 (mtp) cc_final: 0.8811 (mtt) REVERT: L 94 ARG cc_start: 0.7138 (mmm160) cc_final: 0.4607 (mtt-85) REVERT: L 103 ARG cc_start: 0.8258 (tpp-160) cc_final: 0.8003 (tpp-160) REVERT: J 97 LYS cc_start: 0.8431 (mmtt) cc_final: 0.8037 (mttt) REVERT: J 166 ARG cc_start: 0.8026 (mtp-110) cc_final: 0.7792 (mtm110) REVERT: J 246 GLN cc_start: 0.7031 (pt0) cc_final: 0.6378 (pm20) REVERT: N 94 ARG cc_start: 0.7054 (mmm160) cc_final: 0.4506 (mtt-85) REVERT: U 97 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8008 (mttp) REVERT: U 143 ARG cc_start: 0.6412 (tpp-160) cc_final: 0.5823 (mtp85) REVERT: U 153 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7448 (mm-30) REVERT: U 308 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7826 (mpt-90) REVERT: W 100 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8772 (mt0) REVERT: X 94 ARG cc_start: 0.6850 (mmm160) cc_final: 0.4478 (mtt-85) REVERT: X 103 ARG cc_start: 0.8411 (tpp80) cc_final: 0.8144 (tpp-160) outliers start: 41 outliers final: 21 residues processed: 230 average time/residue: 1.4213 time to fit residues: 364.8542 Evaluate side-chains 220 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 290 THR Chi-restraints excluded: chain A residue 375 SER 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 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 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 W residue 100 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 222 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 89 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111480 restraints weight = 22169.345| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.02 r_work: 0.3161 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19722 Z= 0.113 Angle : 0.554 11.066 26919 Z= 0.273 Chirality : 0.044 0.327 3225 Planarity : 0.004 0.034 3276 Dihedral : 5.558 57.658 4275 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.48 % Favored : 96.38 % Rotamer: Outliers : 1.84 % Allowed : 14.15 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2268 helix: 2.30 (0.27), residues: 360 sheet: 0.66 (0.20), residues: 714 loop : -0.33 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 PHE 0.011 0.001 PHE M 29 TYR 0.026 0.001 TYR U 173 ARG 0.010 0.000 ARG A 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 63) link_NAG-ASN : angle 1.75576 ( 189) link_BETA1-4 : bond 0.00377 ( 15) link_BETA1-4 : angle 1.53183 ( 45) link_ALPHA1-3 : bond 0.00986 ( 3) link_ALPHA1-3 : angle 1.20259 ( 9) hydrogen bonds : bond 0.03923 ( 516) hydrogen bonds : angle 4.17092 ( 1368) link_BETA1-6 : bond 0.00360 ( 6) link_BETA1-6 : angle 1.23785 ( 18) SS BOND : bond 0.00430 ( 36) SS BOND : angle 0.87962 ( 72) covalent geometry : bond 0.00259 (19599) covalent geometry : angle 0.52989 (26586) *********************** 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 244 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6365 (mmm) cc_final: 0.5876 (mmm) REVERT: A 173 TYR cc_start: 0.7696 (p90) cc_final: 0.7296 (p90) REVERT: A 375 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8697 (p) REVERT: A 475 MET cc_start: 0.8429 (mmt) cc_final: 0.7587 (mmt) REVERT: B 533 MET cc_start: 0.9148 (mtp) cc_final: 0.8810 (mtt) REVERT: L 94 ARG cc_start: 0.7066 (mmm160) cc_final: 0.4560 (mtt-85) REVERT: L 103 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7960 (tpp-160) REVERT: J 97 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8056 (mttt) REVERT: J 166 ARG cc_start: 0.8092 (mtp-110) cc_final: 0.7795 (mtm110) REVERT: J 208 VAL cc_start: 0.6376 (t) cc_final: 0.6062 (p) REVERT: J 246 GLN cc_start: 0.7012 (pt0) cc_final: 0.6396 (pm20) REVERT: M 52 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7712 (t0) REVERT: N 94 ARG cc_start: 0.7138 (mmm160) cc_final: 0.4471 (mtt-85) REVERT: U 97 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7972 (mttt) REVERT: U 143 ARG cc_start: 0.6476 (tpp-160) cc_final: 0.5955 (mtp85) REVERT: U 153 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7397 (mm-30) REVERT: U 308 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7785 (mpt-90) REVERT: W 100 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8796 (mt0) REVERT: X 94 ARG cc_start: 0.6973 (mmm160) cc_final: 0.4538 (mtt-85) REVERT: X 103 ARG cc_start: 0.8421 (tpp80) cc_final: 0.8143 (tpp-160) outliers start: 37 outliers final: 24 residues processed: 233 average time/residue: 1.4120 time to fit residues: 367.3290 Evaluate side-chains 228 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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 375 SER 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 595 ILE Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain M residue 52 ASN 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 Chi-restraints excluded: chain W residue 100 GLN Chi-restraints excluded: chain X residue 31 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 48 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.148181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109539 restraints weight = 22184.635| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.02 r_work: 0.3150 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19722 Z= 0.160 Angle : 0.603 11.810 26919 Z= 0.299 Chirality : 0.046 0.300 3225 Planarity : 0.004 0.039 3276 Dihedral : 5.681 57.512 4275 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.70 % Favored : 96.21 % Rotamer: Outliers : 1.59 % Allowed : 14.40 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2268 helix: 1.79 (0.27), residues: 378 sheet: 0.69 (0.20), residues: 699 loop : -0.38 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 479 HIS 0.004 0.001 HIS U 352 PHE 0.014 0.002 PHE M 29 TYR 0.025 0.001 TYR U 173 ARG 0.011 0.000 ARG A 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 63) link_NAG-ASN : angle 1.81029 ( 189) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 1.56756 ( 45) link_ALPHA1-3 : bond 0.00862 ( 3) link_ALPHA1-3 : angle 1.18584 ( 9) hydrogen bonds : bond 0.04521 ( 516) hydrogen bonds : angle 4.27084 ( 1368) link_BETA1-6 : bond 0.00317 ( 6) link_BETA1-6 : angle 1.33331 ( 18) SS BOND : bond 0.00506 ( 36) SS BOND : angle 1.03756 ( 72) covalent geometry : bond 0.00382 (19599) covalent geometry : angle 0.57970 (26586) ********************** 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 228 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8329 (mtmt) REVERT: A 142 MET cc_start: 0.6313 (mmm) cc_final: 0.5847 (mmm) REVERT: A 173 TYR cc_start: 0.7690 (p90) cc_final: 0.7305 (p90) REVERT: A 475 MET cc_start: 0.8424 (mmt) cc_final: 0.8218 (mmt) REVERT: B 533 MET cc_start: 0.9145 (mtp) cc_final: 0.8797 (mtt) REVERT: L 94 ARG cc_start: 0.7075 (mmm160) cc_final: 0.4505 (mtt-85) REVERT: L 103 ARG cc_start: 0.8242 (tpp-160) cc_final: 0.7966 (tpp-160) REVERT: J 97 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8026 (mttm) REVERT: J 166 ARG cc_start: 0.8018 (mtp-110) cc_final: 0.7803 (mtm110) REVERT: J 208 VAL cc_start: 0.6445 (t) cc_final: 0.6144 (p) REVERT: J 246 GLN cc_start: 0.7043 (pt0) cc_final: 0.6404 (pm20) REVERT: M 52 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7933 (t0) REVERT: N 94 ARG cc_start: 0.7169 (mmm160) cc_final: 0.4594 (mtt-85) REVERT: U 97 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8064 (mttp) REVERT: U 143 ARG cc_start: 0.6487 (tpp-160) cc_final: 0.5866 (mtp85) REVERT: U 153 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7399 (mm-30) REVERT: U 308 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7838 (mpt-90) REVERT: W 100 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8843 (mt0) REVERT: X 94 ARG cc_start: 0.6972 (mmm160) cc_final: 0.4473 (mtt-85) REVERT: X 103 ARG cc_start: 0.8430 (tpp80) cc_final: 0.8155 (tpp-160) outliers start: 32 outliers final: 26 residues processed: 220 average time/residue: 1.5057 time to fit residues: 370.3695 Evaluate side-chains 224 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 290 THR Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 375 SER 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 595 ILE Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain K residue 639 THR Chi-restraints excluded: chain M residue 52 ASN 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 Chi-restraints excluded: chain W residue 100 GLN Chi-restraints excluded: chain X residue 31 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 15 optimal weight: 3.9990 chunk 168 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.0980 chunk 194 optimal weight: 0.9990 chunk 151 optimal weight: 0.0070 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112922 restraints weight = 22283.926| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.00 r_work: 0.3177 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19722 Z= 0.097 Angle : 0.539 11.019 26919 Z= 0.267 Chirality : 0.043 0.266 3225 Planarity : 0.004 0.040 3276 Dihedral : 5.467 56.981 4275 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.52 % Rotamer: Outliers : 1.64 % Allowed : 14.30 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2268 helix: 2.26 (0.27), residues: 360 sheet: 0.62 (0.20), residues: 714 loop : -0.29 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 PHE 0.009 0.001 PHE A 176 TYR 0.027 0.001 TYR U 173 ARG 0.009 0.000 ARG A 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 63) link_NAG-ASN : angle 1.68714 ( 189) link_BETA1-4 : bond 0.00363 ( 15) link_BETA1-4 : angle 1.48248 ( 45) link_ALPHA1-3 : bond 0.00918 ( 3) link_ALPHA1-3 : angle 1.20944 ( 9) hydrogen bonds : bond 0.03721 ( 516) hydrogen bonds : angle 4.17353 ( 1368) link_BETA1-6 : bond 0.00409 ( 6) link_BETA1-6 : angle 1.20706 ( 18) SS BOND : bond 0.00394 ( 36) SS BOND : angle 0.81467 ( 72) covalent geometry : bond 0.00213 (19599) covalent geometry : angle 0.51698 (26586) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16236.25 seconds wall clock time: 282 minutes 44.78 seconds (16964.78 seconds total)