Starting phenix.real_space_refine on Sat Jul 4 07:41:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t75_25734/07_2026/7t75_25734.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t75_25734/07_2026/7t75_25734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t75_25734/07_2026/7t75_25734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t75_25734/07_2026/7t75_25734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t75_25734/07_2026/7t75_25734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t75_25734/07_2026/7t75_25734.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7t75_25734/07_2026/7t75_25734.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t75_25734/07_2026/7t75_25734.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12024 2.51 5 N 3207 2.21 5 O 3876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19227 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 4.12, per 1000 atoms: 0.21 Number of scatterers: 19227 At special positions: 0 Unit cell: (124.63, 128.75, 149.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3876 8.00 N 3207 7.00 C 12024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.06 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.05 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.05 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.04 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.02 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.02 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS U 119 " - pdb=" SG CYS U 205 " distance=2.06 Simple disulfide: pdb=" SG CYS U 126 " - pdb=" SG CYS U 196 " distance=2.05 Simple disulfide: pdb=" SG CYS U 131 " - pdb=" SG CYS U 157 " distance=2.04 Simple disulfide: pdb=" SG CYS U 218 " - pdb=" SG CYS U 247 " distance=2.05 Simple disulfide: pdb=" SG CYS U 228 " - pdb=" SG CYS U 239 " distance=2.03 Simple disulfide: pdb=" SG CYS U 296 " - pdb=" SG CYS U 331 " distance=2.03 Simple disulfide: pdb=" SG CYS U 378 " - pdb=" SG CYS U 445 " distance=2.04 Simple disulfide: pdb=" SG CYS U 385 " - pdb=" SG CYS U 418 " distance=2.02 Simple disulfide: pdb=" SG CYS U 501 " - pdb=" SG CYS V 605 " distance=2.02 Simple disulfide: pdb=" SG CYS V 598 " - pdb=" SG CYS V 604 " distance=2.02 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA E 3 " - " MAN E 4 " " BMA Q 3 " - " MAN Q 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " BETA1-6 " NAG 2 1 " - " FUC 2 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG 3 1 " - " FUC 3 2 " " NAG G 1 " - " FUC G 2 " " NAG I 1 " - " FUC I 2 " " NAG S 1 " - " FUC S 2 " " NAG T 1 " - " FUC T 2 " NAG-ASN " NAG 0 1 " - " ASN U 262 " " NAG 1 1 " - " ASN U 156 " " NAG 2 1 " - " ASN V 618 " " NAG 3 1 " - " ASN V 611 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 355 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 197 " " NAG A 613 " - " ASN A 133 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 637 " " NAG C 1 " - " ASN A 386 " " NAG D 1 " - " ASN A 332 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 156 " " NAG G 1 " - " ASN B 618 " " NAG I 1 " - " ASN B 611 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 160 " " NAG J 603 " - " ASN J 234 " " NAG J 604 " - " ASN J 137 " " NAG J 605 " - " ASN J 355 " " NAG J 606 " - " ASN J 276 " " NAG J 607 " - " ASN J 392 " " NAG J 608 " - " ASN J 339 " " NAG J 609 " - " ASN J 295 " " NAG J 610 " - " ASN J 448 " " NAG J 611 " - " ASN J 301 " " NAG J 612 " - " ASN J 197 " " NAG J 613 " - " ASN J 133 " " NAG K 701 " - " ASN K 625 " " NAG K 702 " - " ASN K 637 " " NAG O 1 " - " ASN J 386 " " NAG P 1 " - " ASN J 332 " " NAG Q 1 " - " ASN J 262 " " NAG R 1 " - " ASN J 156 " " NAG S 1 " - " ASN K 618 " " NAG T 1 " - " ASN K 611 " " NAG U 601 " - " ASN U 88 " " NAG U 602 " - " ASN U 160 " " NAG U 603 " - " ASN U 234 " " NAG U 604 " - " ASN U 137 " " NAG U 605 " - " ASN U 355 " " NAG U 606 " - " ASN U 276 " " NAG U 607 " - " ASN U 392 " " NAG U 608 " - " ASN U 339 " " NAG U 609 " - " ASN U 295 " " NAG U 610 " - " ASN U 448 " " NAG U 611 " - " ASN U 301 " " NAG U 612 " - " ASN U 197 " " NAG U 613 " - " ASN U 133 " " NAG V 701 " - " ASN V 625 " " NAG V 702 " - " ASN V 637 " " NAG Y 1 " - " ASN U 386 " " NAG Z 1 " - " ASN U 332 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 782.9 milliseconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 20.3% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.554A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 4.085A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.412A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 534 through 540 removed outlier: 3.524A pdb=" N GLN B 538 " --> pdb=" O THR B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 659 removed outlier: 3.740A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'J' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 143 Processing helix chain 'J' and resid 335 through 350 Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.554A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 484 removed outlier: 4.084A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 521 through 526 removed outlier: 4.412A pdb=" N GLY K 525 " --> pdb=" O GLY K 522 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 532 Processing helix chain 'K' and resid 534 through 540 removed outlier: 3.524A pdb=" N GLN K 538 " --> pdb=" O THR K 534 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 596 Processing helix chain 'K' and resid 618 through 624 Processing helix chain 'K' and resid 627 through 636 Processing helix chain 'K' and resid 638 through 659 removed outlier: 3.740A pdb=" N LYS K 655 " --> pdb=" O ASN K 651 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP K 659 " --> pdb=" O LYS K 655 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'U' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU U 102 " --> pdb=" O ASN U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 143 Processing helix chain 'U' and resid 335 through 350 Processing helix chain 'U' and resid 368 through 373 removed outlier: 3.555A pdb=" N THR U 373 " --> pdb=" O LEU U 369 " (cutoff:3.500A) Processing helix chain 'U' and resid 475 through 484 removed outlier: 4.085A pdb=" N GLU U 482 " --> pdb=" O ASN U 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 521 through 526 removed outlier: 4.412A pdb=" N GLY V 525 " --> pdb=" O GLY V 522 " (cutoff:3.500A) Processing helix chain 'V' and resid 527 through 532 Processing helix chain 'V' and resid 534 through 540 removed outlier: 3.524A pdb=" N GLN V 538 " --> pdb=" O THR V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 572 through 596 Processing helix chain 'V' and resid 618 through 624 Processing helix chain 'V' and resid 627 through 636 Processing helix chain 'V' and resid 638 through 659 removed outlier: 3.740A pdb=" N LYS V 655 " --> pdb=" O ASN V 651 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP V 659 " --> pdb=" O LYS V 655 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 32 Processing helix chain 'W' and resid 61 through 64 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'X' and resid 79 through 83 Processing sheet with id=1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.332A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.678A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.405A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.898A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=9, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100H through 103 Processing sheet with id=10, first strand: chain 'L' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 12 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=10 Processing sheet with id=11, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=12, first strand: chain 'J' and resid 494 through 499 removed outlier: 5.332A pdb=" N VAL K 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL J 38 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR K 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR J 40 " --> pdb=" O CYS K 604 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS K 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.678A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=15, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=16, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=17, first strand: chain 'J' and resid 201 through 203 removed outlier: 6.404A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'J' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 259 through 261 current: chain 'J' and resid 284 through 312 removed outlier: 6.898A pdb=" N ASN J 301 " --> pdb=" O ILE J 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE J 323 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 315 through 323A current: chain 'J' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 381 through 385 current: chain 'J' and resid 466 through 470 Processing sheet with id=19, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=20, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=21, first strand: chain 'N' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 12 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=23, first strand: chain 'U' and resid 494 through 499 removed outlier: 5.333A pdb=" N VAL V 608 " --> pdb=" O VAL U 36 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL U 38 " --> pdb=" O THR V 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR V 606 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR U 40 " --> pdb=" O CYS V 604 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS V 604 " --> pdb=" O TYR U 40 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'U' and resid 45 through 47 removed outlier: 3.678A pdb=" N ILE U 225 " --> pdb=" O VAL U 245 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'U' and resid 53 through 55 Processing sheet with id=26, first strand: chain 'U' and resid 91 through 94 Processing sheet with id=27, first strand: chain 'U' and resid 169 through 177 Processing sheet with id=28, first strand: chain 'U' and resid 201 through 203 removed outlier: 6.406A pdb=" N THR U 202 " --> pdb=" O TYR U 435 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'U' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 259 through 261 current: chain 'U' and resid 284 through 312 removed outlier: 6.898A pdb=" N ASN U 301 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE U 323 " --> pdb=" O ASN U 301 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR U 303 " --> pdb=" O GLY U 321 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN U 315 " --> pdb=" O ILE U 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 315 through 323A current: chain 'U' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 381 through 385 current: chain 'U' and resid 466 through 470 Processing sheet with id=30, first strand: chain 'W' and resid 3 through 6 Processing sheet with id=31, first strand: chain 'W' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 11 through 12 current: chain 'W' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 57 through 59 current: chain 'W' and resid 100H through 103 Processing sheet with id=32, first strand: chain 'X' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 12 through 13 current: chain 'X' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 45 through 48 current: chain 'X' and resid 96 through 98 No H-bonds generated for sheet with id=32 Processing sheet with id=33, first strand: chain 'X' and resid 19 through 24 516 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 2.25 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 - 17.51: 10500 17.51 - 35.03: 366 35.03 - 52.54: 108 52.54 - 70.05: 21 70.05 - 87.56: 21 Dihedral angle restraints: 11016 sinusoidal: 4389 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 11013 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: 0.06 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: 2.950 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.120 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 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 : 10.949 87.564 6660 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.79 % Allowed : 2.51 % Favored : 96.69 % Rotamer: Outliers : 0.90 % Allowed : 0.85 % Favored : 98.26 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.17), residues: 2268 helix: -0.64 (0.24), residues: 372 sheet: 0.90 (0.20), residues: 714 loop : 0.58 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 71 TYR 0.064 0.008 TYR L 96 PHE 0.040 0.007 PHE A 353 TRP 0.050 0.009 TRP J 96 HIS 0.012 0.003 HIS J 85 Details of bonding type rmsd/Z covalent geometry : bond 0.02209 / 1.16 (19599) covalent geometry : angle 1.82657 / 1.18 (26586) SS BOND : bond 0.01349 / 0.79 ( 36) SS BOND : angle 3.28449 / 2.21 ( 72) hydrogen bonds : bond 0.17588 / 11.60 ( 516) hydrogen bonds : angle 6.64987 / 4.56 ( 1368) link_ALPHA1-3 : bond 0.07667 / 3.84 ( 3) link_ALPHA1-3 : angle 3.97063 / 2.71 ( 9) link_BETA1-4 : bond 0.07157 / 4.16 ( 15) link_BETA1-4 : angle 4.76798 / 3.38 ( 45) link_BETA1-6 : bond 0.05219 / 3.01 ( 6) link_BETA1-6 : angle 2.60889 / 1.33 ( 18) link_NAG-ASN : bond 0.06887 / 4.33 ( 63) link_NAG-ASN : angle 2.69601 / 1.91 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 414 time to evaluate : 0.711 Fit side-chains REVERT: A 142 MET cc_start: 0.6882 (mmm) cc_final: 0.6439 (mmm) REVERT: L 94 ARG cc_start: 0.6858 (mmm160) cc_final: 0.5554 (mtt180) REVERT: N 94 ARG cc_start: 0.6826 (mmm160) cc_final: 0.5335 (mtt-85) REVERT: U 142 MET cc_start: 0.6788 (mmm) cc_final: 0.6543 (mmm) REVERT: X 94 ARG cc_start: 0.6982 (mmm160) cc_final: 0.5462 (ptp-170) outliers start: 18 outliers final: 4 residues processed: 426 average time/residue: 0.7308 time to fit residues: 342.8522 Evaluate side-chains 231 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain U residue 189 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3761 r_free = 0.3761 target = 0.151311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111815 restraints weight = 22163.461| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.17 r_work: 0.3177 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2218 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= 0.154 Angle : 0.709 11.627 26919 Z= 0.356 Chirality : 0.047 0.267 3225 Planarity : 0.004 0.053 3276 Dihedral : 5.502 58.558 2486 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.38 % Favored : 97.22 % Rotamer: Outliers : 3.14 % Allowed : 9.67 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2268 helix: 1.26 (0.27), residues: 375 sheet: 0.74 (0.19), residues: 708 loop : 0.06 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.011 0.001 TYR X 96 PHE 0.016 0.002 PHE A 176 TRP 0.023 0.002 TRP J 479 HIS 0.004 0.001 HIS J 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (19599) covalent geometry : angle 0.65692 / 0.34 (26586) SS BOND : bond 0.00221 / 0.13 ( 36) SS BOND : angle 1.63785 / 1.03 ( 72) hydrogen bonds : bond 0.05300 / 3.54 ( 516) hydrogen bonds : angle 4.87748 / 3.37 ( 1368) link_ALPHA1-3 : bond 0.00984 / 0.49 ( 3) link_ALPHA1-3 : angle 1.27344 / 0.79 ( 9) link_BETA1-4 : bond 0.00613 / 0.39 ( 15) link_BETA1-4 : angle 2.47778 / 1.73 ( 45) link_BETA1-6 : bond 0.00682 / 0.35 ( 6) link_BETA1-6 : angle 0.97958 / 0.54 ( 18) link_NAG-ASN : bond 0.00287 / 0.19 ( 63) link_NAG-ASN : angle 2.88520 / 2.08 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8948 (mtp) cc_final: 0.8670 (mtp) REVERT: A 142 MET cc_start: 0.6351 (mmm) cc_final: 0.5718 (mmm) REVERT: A 412 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6574 (t0) REVERT: L 94 ARG cc_start: 0.7288 (mmm160) cc_final: 0.4810 (mtt180) REVERT: J 97 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7949 (mttt) REVERT: J 166 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7717 (mtm110) REVERT: J 246 GLN cc_start: 0.6926 (pm20) cc_final: 0.6721 (mm-40) REVERT: J 348 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7576 (mp-120) REVERT: M 23 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6668 (tmt170) REVERT: N 94 ARG cc_start: 0.7192 (mmm160) cc_final: 0.4704 (mtt-85) REVERT: U 83 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: U 97 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7986 (mttp) REVERT: U 102 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7632 (mp0) REVERT: U 106 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: U 142 MET cc_start: 0.6661 (mmm) cc_final: 0.6274 (mmm) REVERT: U 143 ARG cc_start: 0.6551 (tpp-160) cc_final: 0.5976 (mtp85) REVERT: U 153 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7543 (mm-30) REVERT: U 348 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.6660 (mp-120) REVERT: W 23 ARG cc_start: 0.8312 (tmt170) cc_final: 0.8019 (tmt170) REVERT: W 100 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8337 (p) REVERT: X 94 ARG cc_start: 0.7170 (mmm160) cc_final: 0.4652 (mtt180) REVERT: X 103 ARG cc_start: 0.7665 (tpp-160) cc_final: 0.7429 (tpp-160) outliers start: 63 outliers final: 29 residues processed: 296 average time/residue: 0.6920 time to fit residues: 227.0250 Evaluate side-chains 237 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 A residue 412 ASP 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 M residue 23 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 83 GLU Chi-restraints excluded: chain U residue 106 GLU Chi-restraints excluded: chain U residue 138 ILE Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 348 GLN Chi-restraints excluded: chain U residue 371 VAL Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 128 optimal weight: 7.9990 chunk 164 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3768 r_free = 0.3768 target = 0.152180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114073 restraints weight = 22465.970| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.04 r_work: 0.3212 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19722 Z= 0.120 Angle : 0.597 9.378 26919 Z= 0.299 Chirality : 0.044 0.280 3225 Planarity : 0.004 0.044 3276 Dihedral : 5.237 59.946 2486 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.73 % Favored : 97.00 % Rotamer: Outliers : 2.84 % Allowed : 10.66 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2268 helix: 2.10 (0.27), residues: 357 sheet: 0.67 (0.19), residues: 717 loop : -0.12 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 143 TYR 0.020 0.001 TYR A 173 PHE 0.012 0.002 PHE M 29 TRP 0.020 0.001 TRP J 479 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (19599) covalent geometry : angle 0.56354 / 0.29 (26586) SS BOND : bond 0.00468 / 0.29 ( 36) SS BOND : angle 1.27333 / 0.87 ( 72) hydrogen bonds : bond 0.04231 / 2.83 ( 516) hydrogen bonds : angle 4.46466 / 3.10 ( 1368) link_ALPHA1-3 : bond 0.00890 / 0.45 ( 3) link_ALPHA1-3 : angle 1.40600 / 0.98 ( 9) link_BETA1-4 : bond 0.00579 / 0.35 ( 15) link_BETA1-4 : angle 1.71116 / 1.19 ( 45) link_BETA1-6 : bond 0.00435 / 0.22 ( 6) link_BETA1-6 : angle 1.10631 / 0.66 ( 18) link_NAG-ASN : bond 0.00280 / 0.17 ( 63) link_NAG-ASN : angle 2.12265 / 1.52 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8911 (mtp) cc_final: 0.8554 (mtp) REVERT: A 142 MET cc_start: 0.6427 (mmm) cc_final: 0.5665 (mmm) REVERT: A 153 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7037 (mt-10) REVERT: A 208 VAL cc_start: 0.6494 (t) cc_final: 0.6198 (p) REVERT: A 412 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6835 (t0) REVERT: B 533 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8698 (mtt) REVERT: L 94 ARG cc_start: 0.7194 (mmm160) cc_final: 0.4665 (mtt-85) REVERT: J 97 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7865 (mttt) REVERT: J 166 ARG cc_start: 0.7879 (mtp-110) cc_final: 0.7483 (mtm110) REVERT: J 208 VAL cc_start: 0.6544 (t) cc_final: 0.6270 (p) REVERT: K 616 ASN cc_start: 0.8390 (p0) cc_final: 0.7942 (t0) REVERT: M 23 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6604 (tmt170) REVERT: N 94 ARG cc_start: 0.7118 (mmm160) cc_final: 0.4555 (mtt-85) REVERT: U 97 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7882 (mttp) REVERT: U 142 MET cc_start: 0.6621 (mmm) cc_final: 0.6253 (mmm) REVERT: U 143 ARG cc_start: 0.6455 (tpp-160) cc_final: 0.5965 (mtp85) REVERT: U 153 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7425 (mm-30) REVERT: W 100 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8249 (p) REVERT: X 74 THR cc_start: 0.8371 (m) cc_final: 0.8123 (m) REVERT: X 94 ARG cc_start: 0.7121 (mmm160) cc_final: 0.4669 (mtt180) outliers start: 57 outliers final: 28 residues processed: 259 average time/residue: 0.6679 time to fit residues: 192.3535 Evaluate side-chains 230 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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 U residue 465 THR 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 188 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 133 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 0.0370 chunk 170 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN M 52 ASN U 258 GLN U 348 GLN X 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112181 restraints weight = 22221.227| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.03 r_work: 0.3177 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2919 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= 0.129 Angle : 0.577 9.973 26919 Z= 0.289 Chirality : 0.044 0.272 3225 Planarity : 0.004 0.036 3276 Dihedral : 5.085 59.635 2486 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.82 % Favored : 96.91 % Rotamer: Outliers : 3.39 % Allowed : 10.81 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2268 helix: 2.22 (0.27), residues: 360 sheet: 0.61 (0.19), residues: 717 loop : -0.21 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 143 TYR 0.020 0.001 TYR A 173 PHE 0.014 0.002 PHE M 29 TRP 0.021 0.001 TRP J 479 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (19599) covalent geometry : angle 0.55366 / 0.28 (26586) SS BOND : bond 0.00470 / 0.30 ( 36) SS BOND : angle 1.08502 / 0.71 ( 72) hydrogen bonds : bond 0.04200 / 2.82 ( 516) hydrogen bonds : angle 4.31537 / 3.00 ( 1368) link_ALPHA1-3 : bond 0.00695 / 0.35 ( 3) link_ALPHA1-3 : angle 1.33202 / 0.92 ( 9) link_BETA1-4 : bond 0.00488 / 0.30 ( 15) link_BETA1-4 : angle 1.50900 / 1.03 ( 45) link_BETA1-6 : bond 0.00313 / 0.17 ( 6) link_BETA1-6 : angle 1.18823 / 0.70 ( 18) link_NAG-ASN : bond 0.00228 / 0.14 ( 63) link_NAG-ASN : angle 1.76046 / 1.25 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8169 (mtmt) REVERT: A 142 MET cc_start: 0.6412 (mmm) cc_final: 0.5963 (mmm) REVERT: A 208 VAL cc_start: 0.6511 (t) cc_final: 0.6207 (p) REVERT: A 412 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6489 (t0) REVERT: A 428 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6452 (mt0) REVERT: A 475 MET cc_start: 0.8305 (mmp) cc_final: 0.8018 (mmt) REVERT: B 533 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8773 (mtt) REVERT: L 94 ARG cc_start: 0.7169 (mmm160) cc_final: 0.4638 (mtt-85) REVERT: J 97 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7818 (mttp) REVERT: J 106 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: J 166 ARG cc_start: 0.7914 (mtp-110) cc_final: 0.7532 (mtm110) REVERT: J 208 VAL cc_start: 0.6502 (t) cc_final: 0.6215 (p) REVERT: K 533 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8743 (mtp) REVERT: M 23 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6611 (tmt170) REVERT: N 94 ARG cc_start: 0.7107 (mmm160) cc_final: 0.4538 (mtt-85) REVERT: N 103 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7966 (tpp-160) REVERT: U 97 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7893 (mttp) REVERT: U 142 MET cc_start: 0.6590 (mmm) cc_final: 0.6094 (mmm) REVERT: U 143 ARG cc_start: 0.6359 (tpp-160) cc_final: 0.5817 (mtp85) REVERT: U 153 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7453 (mm-30) REVERT: X 27 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7093 (m-30) REVERT: X 94 ARG cc_start: 0.7030 (mmm160) cc_final: 0.4590 (mtt180) outliers start: 68 outliers final: 32 residues processed: 260 average time/residue: 0.6567 time to fit residues: 189.7787 Evaluate side-chains 234 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 K residue 533 MET Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain U residue 138 ILE Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 371 VAL Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain U residue 465 THR Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 612 SER Chi-restraints excluded: chain X residue 27 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 7 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 204 optimal weight: 0.0470 chunk 140 optimal weight: 0.0670 chunk 178 optimal weight: 0.2980 chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 246 GLN A 348 GLN J 103 GLN M 52 ASN U 103 GLN U 348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113697 restraints weight = 22282.875| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.02 r_work: 0.3209 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3109 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= 0.100 Angle : 0.535 10.601 26919 Z= 0.266 Chirality : 0.043 0.265 3225 Planarity : 0.003 0.034 3276 Dihedral : 4.863 59.507 2486 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.65 % Favored : 97.09 % Rotamer: Outliers : 2.49 % Allowed : 12.46 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2268 helix: 2.40 (0.27), residues: 360 sheet: 0.65 (0.19), residues: 726 loop : -0.22 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 143 TYR 0.021 0.001 TYR A 173 PHE 0.010 0.001 PHE M 29 TRP 0.021 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (19599) covalent geometry : angle 0.51285 / 0.26 (26586) SS BOND : bond 0.00420 / 0.26 ( 36) SS BOND : angle 0.87878 / 0.56 ( 72) hydrogen bonds : bond 0.03662 / 2.46 ( 516) hydrogen bonds : angle 4.19220 / 2.92 ( 1368) link_ALPHA1-3 : bond 0.00666 / 0.33 ( 3) link_ALPHA1-3 : angle 1.36835 / 0.98 ( 9) link_BETA1-4 : bond 0.00454 / 0.28 ( 15) link_BETA1-4 : angle 1.35668 / 0.91 ( 45) link_BETA1-6 : bond 0.00357 / 0.19 ( 6) link_BETA1-6 : angle 1.12326 / 0.65 ( 18) link_NAG-ASN : bond 0.00217 / 0.14 ( 63) link_NAG-ASN : angle 1.66361 / 1.19 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6415 (mmm) cc_final: 0.5968 (mmm) REVERT: A 208 VAL cc_start: 0.6552 (t) cc_final: 0.6255 (p) REVERT: A 375 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8625 (p) REVERT: A 428 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6450 (mt0) REVERT: B 533 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8735 (mtt) REVERT: L 94 ARG cc_start: 0.7127 (mmm160) cc_final: 0.4659 (mtt180) REVERT: J 97 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7756 (mttp) REVERT: J 166 ARG cc_start: 0.7888 (mtp-110) cc_final: 0.7541 (mtm110) REVERT: J 208 VAL cc_start: 0.6483 (t) cc_final: 0.6188 (p) REVERT: K 533 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8735 (mtp) REVERT: M 23 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6550 (tmt170) REVERT: M 52 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7261 (t0) REVERT: N 85 ASP cc_start: 0.8515 (m-30) cc_final: 0.8281 (m-30) REVERT: N 94 ARG cc_start: 0.7036 (mmm160) cc_final: 0.4470 (mtt-85) REVERT: N 103 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7985 (tpp-160) REVERT: U 97 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7868 (mttp) REVERT: U 142 MET cc_start: 0.6729 (mmm) cc_final: 0.6229 (mmm) REVERT: U 143 ARG cc_start: 0.6348 (tpp-160) cc_final: 0.5798 (mtp85) REVERT: U 153 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7389 (mm-30) REVERT: X 27 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: X 94 ARG cc_start: 0.6963 (mmm160) cc_final: 0.4551 (mtt-85) outliers start: 50 outliers final: 29 residues processed: 238 average time/residue: 0.6955 time to fit residues: 184.0615 Evaluate side-chains 236 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 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 333 VAL Chi-restraints excluded: chain J residue 426 MET Chi-restraints excluded: chain K residue 533 MET 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 M residue 52 ASN 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 333 VAL Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain U residue 465 THR Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain X residue 27 ASP Chi-restraints excluded: chain X residue 31 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 105 optimal weight: 1.9990 chunk 209 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 246 GLN A 348 GLN J 348 GLN M 52 ASN U 348 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116854 restraints weight = 21973.838| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.72 r_work: 0.3048 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 19722 Z= 0.203 Angle : 0.649 9.867 26919 Z= 0.323 Chirality : 0.047 0.270 3225 Planarity : 0.004 0.036 3276 Dihedral : 5.236 58.905 2486 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.22 % Favored : 96.52 % Rotamer: Outliers : 3.04 % Allowed : 12.36 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2268 helix: 1.78 (0.27), residues: 378 sheet: 0.65 (0.19), residues: 720 loop : -0.33 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 143 TYR 0.021 0.002 TYR U 173 PHE 0.016 0.002 PHE M 29 TRP 0.026 0.002 TRP J 479 HIS 0.005 0.002 HIS U 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (19599) covalent geometry : angle 0.62721 / 0.32 (26586) SS BOND : bond 0.00573 / 0.36 ( 36) SS BOND : angle 1.20718 / 0.78 ( 72) hydrogen bonds : bond 0.05095 / 3.42 ( 516) hydrogen bonds : angle 4.40581 / 3.06 ( 1368) link_ALPHA1-3 : bond 0.00760 / 0.38 ( 3) link_ALPHA1-3 : angle 1.39046 / 0.97 ( 9) link_BETA1-4 : bond 0.00415 / 0.25 ( 15) link_BETA1-4 : angle 1.50489 / 1.02 ( 45) link_BETA1-6 : bond 0.00208 / 0.10 ( 6) link_BETA1-6 : angle 1.42113 / 0.84 ( 18) link_NAG-ASN : bond 0.00221 / 0.14 ( 63) link_NAG-ASN : angle 1.79553 / 1.28 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 198 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6380 (mmm) cc_final: 0.5864 (mmm) REVERT: A 412 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6529 (t0) REVERT: A 428 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6752 (mt0) REVERT: A 475 MET cc_start: 0.8561 (mmp) cc_final: 0.8254 (mmt) REVERT: B 533 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8856 (mtp) REVERT: B 633 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8250 (mtpt) REVERT: L 94 ARG cc_start: 0.7289 (mmm160) cc_final: 0.4642 (mtt-85) REVERT: J 97 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8021 (mttm) REVERT: J 166 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7800 (mtm110) REVERT: J 208 VAL cc_start: 0.6495 (t) cc_final: 0.6199 (p) REVERT: J 246 GLN cc_start: 0.7267 (pt0) cc_final: 0.6525 (pm20) REVERT: N 85 ASP cc_start: 0.8590 (m-30) cc_final: 0.8385 (m-30) REVERT: N 94 ARG cc_start: 0.7194 (mmm160) cc_final: 0.4458 (mtt-85) REVERT: U 97 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8039 (mttp) REVERT: U 143 ARG cc_start: 0.6389 (tpp-160) cc_final: 0.5772 (mtp85) REVERT: U 153 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7564 (mm-30) REVERT: W 46 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: X 27 ASP cc_start: 0.7557 (m-30) cc_final: 0.7303 (m-30) REVERT: X 94 ARG cc_start: 0.7176 (mmm160) cc_final: 0.4539 (mtt-85) REVERT: X 103 ARG cc_start: 0.8438 (tpp80) cc_final: 0.8198 (tpp-160) outliers start: 61 outliers final: 33 residues processed: 238 average time/residue: 0.6368 time to fit residues: 168.5954 Evaluate side-chains 233 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 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 633 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 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 K residue 612 SER Chi-restraints excluded: chain M residue 97 MET 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 333 VAL Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain U residue 465 THR 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 46 GLU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 31 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 45 optimal weight: 0.6980 chunk 224 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 138 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3739 r_free = 0.3739 target = 0.149767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111578 restraints weight = 22291.886| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.01 r_work: 0.3172 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3301 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= 0.115 Angle : 0.550 10.493 26919 Z= 0.273 Chirality : 0.043 0.261 3225 Planarity : 0.004 0.038 3276 Dihedral : 4.904 58.408 2484 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.82 % Favored : 96.96 % Rotamer: Outliers : 2.09 % Allowed : 13.35 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2268 helix: 2.28 (0.27), residues: 360 sheet: 0.57 (0.19), residues: 732 loop : -0.26 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 143 TYR 0.023 0.001 TYR U 173 PHE 0.012 0.001 PHE M 29 TRP 0.026 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (19599) covalent geometry : angle 0.52998 / 0.27 (26586) SS BOND : bond 0.00450 / 0.29 ( 36) SS BOND : angle 0.92110 / 0.59 ( 72) hydrogen bonds : bond 0.03941 / 2.64 ( 516) hydrogen bonds : angle 4.22789 / 2.94 ( 1368) link_ALPHA1-3 : bond 0.00722 / 0.36 ( 3) link_ALPHA1-3 : angle 1.46274 / 1.03 ( 9) link_BETA1-4 : bond 0.00408 / 0.25 ( 15) link_BETA1-4 : angle 1.31901 / 0.89 ( 45) link_BETA1-6 : bond 0.00374 / 0.18 ( 6) link_BETA1-6 : angle 1.21706 / 0.69 ( 18) link_NAG-ASN : bond 0.00218 / 0.14 ( 63) link_NAG-ASN : angle 1.60875 / 1.13 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6375 (mmm) cc_final: 0.5860 (mmm) REVERT: A 375 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8641 (p) REVERT: A 428 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6605 (mt0) REVERT: A 475 MET cc_start: 0.8413 (mmp) cc_final: 0.8196 (mmt) REVERT: B 533 MET cc_start: 0.9133 (mtp) cc_final: 0.8786 (mtt) REVERT: L 94 ARG cc_start: 0.7115 (mmm160) cc_final: 0.4578 (mtt-85) REVERT: J 97 LYS cc_start: 0.8379 (mmtt) cc_final: 0.7936 (mttt) REVERT: J 166 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7667 (mtm110) REVERT: J 208 VAL cc_start: 0.6422 (t) cc_final: 0.6117 (p) REVERT: J 246 GLN cc_start: 0.7058 (pt0) cc_final: 0.6371 (pm20) REVERT: M 52 ASN cc_start: 0.7881 (t0) cc_final: 0.7523 (t0) REVERT: M 97 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7795 (mtm) REVERT: N 94 ARG cc_start: 0.6923 (mmm160) cc_final: 0.4469 (mtt-85) REVERT: U 97 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7929 (mttp) REVERT: U 143 ARG cc_start: 0.6380 (tpp-160) cc_final: 0.5818 (mtp85) REVERT: U 153 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7472 (mm-30) REVERT: U 308 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7840 (mpt-90) REVERT: X 27 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: X 94 ARG cc_start: 0.6896 (mmm160) cc_final: 0.4463 (mtt-85) REVERT: X 103 ARG cc_start: 0.8393 (tpp80) cc_final: 0.8143 (tpp-160) outliers start: 42 outliers final: 24 residues processed: 233 average time/residue: 0.6536 time to fit residues: 169.5129 Evaluate side-chains 226 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 375 SER Chi-restraints excluded: chain A residue 428 GLN 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 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 97 MET 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 308 ARG Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain U residue 465 THR Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain X residue 27 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 161 optimal weight: 3.9990 chunk 93 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 152 optimal weight: 5.9990 chunk 145 optimal weight: 0.0370 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN J 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 = 0.3749 r_free = 0.3749 target = 0.150558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112528 restraints weight = 22190.431| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.01 r_work: 0.3196 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3411 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= 0.102 Angle : 0.533 11.001 26919 Z= 0.263 Chirality : 0.043 0.263 3225 Planarity : 0.004 0.033 3276 Dihedral : 4.700 57.633 2484 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.26 % Favored : 96.56 % Rotamer: Outliers : 2.04 % Allowed : 13.40 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 2268 helix: 2.41 (0.27), residues: 360 sheet: 0.53 (0.19), residues: 753 loop : -0.18 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 143 TYR 0.025 0.001 TYR U 173 PHE 0.010 0.001 PHE M 29 TRP 0.026 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (19599) covalent geometry : angle 0.51558 / 0.26 (26586) SS BOND : bond 0.00410 / 0.26 ( 36) SS BOND : angle 0.85081 / 0.54 ( 72) hydrogen bonds : bond 0.03692 / 2.49 ( 516) hydrogen bonds : angle 4.11914 / 2.87 ( 1368) link_ALPHA1-3 : bond 0.00687 / 0.34 ( 3) link_ALPHA1-3 : angle 1.45769 / 1.03 ( 9) link_BETA1-4 : bond 0.00395 / 0.24 ( 15) link_BETA1-4 : angle 1.27484 / 0.85 ( 45) link_BETA1-6 : bond 0.00367 / 0.18 ( 6) link_BETA1-6 : angle 1.21389 / 0.70 ( 18) link_NAG-ASN : bond 0.00203 / 0.13 ( 63) link_NAG-ASN : angle 1.47714 / 1.04 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6375 (mmm) cc_final: 0.5863 (mmm) REVERT: A 173 TYR cc_start: 0.7594 (p90) cc_final: 0.7185 (p90) REVERT: A 375 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 533 MET cc_start: 0.9145 (mtp) cc_final: 0.8797 (mtt) REVERT: L 94 ARG cc_start: 0.7039 (mmm160) cc_final: 0.4484 (mtt-85) REVERT: J 97 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7950 (mttt) REVERT: J 166 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7673 (mtm110) REVERT: J 208 VAL cc_start: 0.6395 (t) cc_final: 0.6070 (p) REVERT: J 246 GLN cc_start: 0.6989 (pt0) cc_final: 0.6263 (pm20) REVERT: N 94 ARG cc_start: 0.6887 (mmm160) cc_final: 0.4412 (mtt-85) REVERT: U 97 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7914 (mttt) REVERT: U 143 ARG cc_start: 0.6448 (tpp-160) cc_final: 0.5965 (mtp85) REVERT: U 153 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7455 (mm-30) REVERT: U 308 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7837 (mpt-90) REVERT: X 94 ARG cc_start: 0.6903 (mmm160) cc_final: 0.4534 (mtt-85) REVERT: X 103 ARG cc_start: 0.8367 (tpp80) cc_final: 0.8114 (tpp-160) outliers start: 41 outliers final: 25 residues processed: 235 average time/residue: 0.6361 time to fit residues: 166.3640 Evaluate side-chains 229 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 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 H residue 82 MET 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 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 U residue 465 THR Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 612 SER Chi-restraints excluded: chain X residue 31 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 164 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 348 GLN J 103 GLN J 348 GLN 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 = 0.3705 r_free = 0.3705 target = 0.146596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116520 restraints weight = 21943.286| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.71 r_work: 0.3072 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19722 Z= 0.209 Angle : 0.652 10.472 26919 Z= 0.324 Chirality : 0.047 0.264 3225 Planarity : 0.004 0.035 3276 Dihedral : 5.136 57.916 2484 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.44 % Favored : 96.43 % Rotamer: Outliers : 2.19 % Allowed : 13.40 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2268 helix: 1.65 (0.27), residues: 378 sheet: 0.67 (0.20), residues: 708 loop : -0.38 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 143 TYR 0.023 0.002 TYR U 173 PHE 0.017 0.002 PHE M 29 TRP 0.030 0.002 TRP J 479 HIS 0.005 0.001 HIS U 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (19599) covalent geometry : angle 0.63182 / 0.32 (26586) SS BOND : bond 0.00568 / 0.36 ( 36) SS BOND : angle 1.21218 / 0.78 ( 72) hydrogen bonds : bond 0.05134 / 3.45 ( 516) hydrogen bonds : angle 4.38292 / 3.05 ( 1368) link_ALPHA1-3 : bond 0.00680 / 0.34 ( 3) link_ALPHA1-3 : angle 1.44282 / 1.02 ( 9) link_BETA1-4 : bond 0.00377 / 0.23 ( 15) link_BETA1-4 : angle 1.44619 / 0.98 ( 45) link_BETA1-6 : bond 0.00207 / 0.09 ( 6) link_BETA1-6 : angle 1.50961 / 0.87 ( 18) link_NAG-ASN : bond 0.00217 / 0.14 ( 63) link_NAG-ASN : angle 1.72343 / 1.23 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6388 (mmm) cc_final: 0.5906 (mmm) REVERT: A 360 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7292 (ttp80) REVERT: A 475 MET cc_start: 0.8563 (mmp) cc_final: 0.7705 (mmt) REVERT: B 533 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8917 (mtt) REVERT: L 31 ASN cc_start: 0.8823 (m110) cc_final: 0.8548 (m-40) REVERT: L 94 ARG cc_start: 0.7217 (mmm160) cc_final: 0.4656 (mtt-85) REVERT: J 97 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8070 (mttt) REVERT: J 166 ARG cc_start: 0.8121 (mtp-110) cc_final: 0.7890 (mtm110) REVERT: J 208 VAL cc_start: 0.6390 (t) cc_final: 0.6098 (p) REVERT: J 246 GLN cc_start: 0.7164 (pt0) cc_final: 0.6521 (pm20) REVERT: N 94 ARG cc_start: 0.7296 (mmm160) cc_final: 0.4509 (mtt-85) REVERT: U 97 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8036 (mttt) REVERT: U 143 ARG cc_start: 0.6541 (tpp-160) cc_final: 0.5990 (mtp85) REVERT: U 153 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7533 (mm-30) REVERT: U 231 LYS cc_start: 0.8469 (mmtm) cc_final: 0.7978 (mppt) REVERT: U 308 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7980 (mpt-90) REVERT: X 94 ARG cc_start: 0.7127 (mmm160) cc_final: 0.4606 (mtt-85) REVERT: X 103 ARG cc_start: 0.8481 (tpp80) cc_final: 0.8225 (tpp-160) outliers start: 44 outliers final: 35 residues processed: 230 average time/residue: 0.6408 time to fit residues: 164.1105 Evaluate side-chains 233 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 348 GLN Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 581 LEU 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 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 K residue 612 SER Chi-restraints excluded: chain K residue 639 THR Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 184 MET 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 U residue 465 THR Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 612 SER 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 156 optimal weight: 0.0070 chunk 38 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 123 optimal weight: 0.0040 chunk 68 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 134 optimal weight: 0.2980 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN J 348 GLN N 31 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 = 0.3753 r_free = 0.3753 target = 0.150932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113083 restraints weight = 22157.729| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.00 r_work: 0.3200 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19722 Z= 0.095 Angle : 0.543 12.789 26919 Z= 0.267 Chirality : 0.044 0.417 3225 Planarity : 0.004 0.037 3276 Dihedral : 4.709 56.717 2484 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 1.59 % Allowed : 14.10 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2268 helix: 2.27 (0.27), residues: 360 sheet: 0.59 (0.19), residues: 741 loop : -0.23 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 143 TYR 0.027 0.001 TYR U 173 PHE 0.009 0.001 PHE A 176 TRP 0.026 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (19599) covalent geometry : angle 0.52300 / 0.26 (26586) SS BOND : bond 0.00383 / 0.24 ( 36) SS BOND : angle 0.80456 / 0.51 ( 72) hydrogen bonds : bond 0.03606 / 2.41 ( 516) hydrogen bonds : angle 4.17204 / 2.91 ( 1368) link_ALPHA1-3 : bond 0.00708 / 0.35 ( 3) link_ALPHA1-3 : angle 1.52500 / 1.09 ( 9) link_BETA1-4 : bond 0.00417 / 0.25 ( 15) link_BETA1-4 : angle 1.25814 / 0.85 ( 45) link_BETA1-6 : bond 0.00435 / 0.22 ( 6) link_BETA1-6 : angle 1.14869 / 0.64 ( 18) link_NAG-ASN : bond 0.00265 / 0.17 ( 63) link_NAG-ASN : angle 1.62966 / 1.17 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6371 (mmm) cc_final: 0.5875 (mmm) REVERT: A 173 TYR cc_start: 0.7523 (p90) cc_final: 0.7148 (p90) REVERT: A 375 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8662 (p) REVERT: A 475 MET cc_start: 0.8362 (mmp) cc_final: 0.8051 (mmt) REVERT: B 533 MET cc_start: 0.9128 (mtp) cc_final: 0.8786 (mtt) REVERT: L 31 ASN cc_start: 0.8542 (m110) cc_final: 0.8236 (m-40) REVERT: L 94 ARG cc_start: 0.7026 (mmm160) cc_final: 0.4495 (mtt-85) REVERT: J 97 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7992 (mttt) REVERT: J 166 ARG cc_start: 0.8039 (mtp-110) cc_final: 0.7757 (mtm110) REVERT: J 246 GLN cc_start: 0.7025 (pt0) cc_final: 0.6302 (pm20) REVERT: N 94 ARG cc_start: 0.6980 (mmm160) cc_final: 0.4499 (mtt-85) REVERT: U 97 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8001 (mttp) REVERT: U 143 ARG cc_start: 0.6573 (tpp-160) cc_final: 0.5975 (mtp85) REVERT: U 153 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7444 (mm-30) REVERT: U 308 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7793 (mpt-90) REVERT: W 23 ARG cc_start: 0.8115 (tmt170) cc_final: 0.7888 (tmt170) REVERT: X 94 ARG cc_start: 0.6860 (mmm160) cc_final: 0.4518 (mtt-85) REVERT: X 103 ARG cc_start: 0.8426 (tpp80) cc_final: 0.8155 (tpp-160) outliers start: 32 outliers final: 19 residues processed: 228 average time/residue: 0.6532 time to fit residues: 165.8305 Evaluate side-chains 213 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 141 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE 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 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 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 465 THR Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 129 optimal weight: 0.0980 chunk 209 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 74 optimal weight: 0.1980 chunk 106 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 348 GLN J 348 GLN U 348 GLN X 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112372 restraints weight = 22192.311| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.00 r_work: 0.3187 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3549 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= 0.106 Angle : 0.549 11.675 26919 Z= 0.269 Chirality : 0.044 0.330 3225 Planarity : 0.004 0.040 3276 Dihedral : 4.629 55.706 2484 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.60 % Rotamer: Outliers : 1.30 % Allowed : 14.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2268 helix: 2.33 (0.27), residues: 360 sheet: 0.63 (0.20), residues: 738 loop : -0.26 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 143 TYR 0.026 0.001 TYR U 173 PHE 0.011 0.001 PHE M 29 TRP 0.027 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (19599) covalent geometry : angle 0.52970 / 0.27 (26586) SS BOND : bond 0.00416 / 0.26 ( 36) SS BOND : angle 0.87045 / 0.55 ( 72) hydrogen bonds : bond 0.03757 / 2.53 ( 516) hydrogen bonds : angle 4.12044 / 2.87 ( 1368) link_ALPHA1-3 : bond 0.00663 / 0.33 ( 3) link_ALPHA1-3 : angle 1.48533 / 1.06 ( 9) link_BETA1-4 : bond 0.00389 / 0.23 ( 15) link_BETA1-4 : angle 1.26955 / 0.85 ( 45) link_BETA1-6 : bond 0.00356 / 0.18 ( 6) link_BETA1-6 : angle 1.23527 / 0.71 ( 18) link_NAG-ASN : bond 0.00195 / 0.12 ( 63) link_NAG-ASN : angle 1.58530 / 1.14 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7028.82 seconds wall clock time: 120 minutes 23.70 seconds (7223.70 seconds total)