Starting phenix.real_space_refine on Sun Sep 13 01:20:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x9u_22111/09_2026/6x9u_22111.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x9u_22111/09_2026/6x9u_22111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x9u_22111/09_2026/6x9u_22111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x9u_22111/09_2026/6x9u_22111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x9u_22111/09_2026/6x9u_22111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x9u_22111/09_2026/6x9u_22111.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x9u_22111/09_2026/6x9u_22111.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x9u_22111/09_2026/6x9u_22111.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 12258 2.51 5 N 3273 2.21 5 O 3933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19590 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "T" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "U" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "V" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "T" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.57, per 1000 atoms: 0.23 Number of scatterers: 19590 At special positions: 0 Unit cell: (124.63, 122.57, 150.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3933 8.00 N 3273 7.00 C 12258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.12 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.13 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.12 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.14 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.05 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 119 " - pdb=" SG CYS S 205 " distance=2.04 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.04 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.12 Simple disulfide: pdb=" SG CYS S 296 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 378 " - pdb=" SG CYS S 445 " distance=2.02 Simple disulfide: pdb=" SG CYS S 385 " - pdb=" SG CYS S 418 " distance=2.02 Simple disulfide: pdb=" SG CYS S 501 " - pdb=" SG CYS T 605 " distance=2.13 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.02 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.05 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG 0 1 " - " ASN S 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 606 " - " ASN A 160 " " NAG A 609 " - " ASN A 234 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 295 " " NAG A 616 " - " ASN A 301 " " NAG A 617 " - " ASN A 332 " " NAG A 618 " - " ASN A 339 " " NAG A 619 " - " ASN A 355 " " NAG A 620 " - " ASN A 363 " " NAG A 623 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 1 " - " ASN A 156 " " NAG D 1 " - " ASN A 197 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 137 " " NAG I 606 " - " ASN I 160 " " NAG I 609 " - " ASN I 234 " " NAG I 614 " - " ASN I 276 " " NAG I 615 " - " ASN I 295 " " NAG I 616 " - " ASN I 301 " " NAG I 617 " - " ASN I 332 " " NAG I 618 " - " ASN I 339 " " NAG I 619 " - " ASN I 355 " " NAG I 620 " - " ASN I 363 " " NAG I 623 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG J 703 " - " ASN J 625 " " NAG J 704 " - " ASN J 637 " " NAG N 1 " - " ASN I 156 " " NAG O 1 " - " ASN I 197 " " NAG P 1 " - " ASN I 262 " " NAG Q 1 " - " ASN I 386 " " NAG R 1 " - " ASN I 448 " " NAG S 601 " - " ASN S 88 " " NAG S 602 " - " ASN S 133 " " NAG S 603 " - " ASN S 137 " " NAG S 606 " - " ASN S 160 " " NAG S 609 " - " ASN S 234 " " NAG S 614 " - " ASN S 276 " " NAG S 615 " - " ASN S 295 " " NAG S 616 " - " ASN S 301 " " NAG S 617 " - " ASN S 332 " " NAG S 618 " - " ASN S 339 " " NAG S 619 " - " ASN S 355 " " NAG S 620 " - " ASN S 363 " " NAG S 623 " - " ASN S 392 " " NAG T 701 " - " ASN T 611 " " NAG T 702 " - " ASN T 618 " " NAG T 703 " - " ASN T 625 " " NAG T 704 " - " ASN T 637 " " NAG W 1 " - " ASN S 156 " " NAG X 1 " - " ASN S 197 " " NAG Y 1 " - " ASN S 262 " " NAG Z 1 " - " ASN S 386 " Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 48 sheets defined 21.4% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.093A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.108A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.796A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.472A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.557A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 removed outlier: 3.531A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.093A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 4.109A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.796A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 removed outlier: 4.473A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.556A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 removed outlier: 3.531A pdb=" N GLN J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'S' and resid 98 through 115 removed outlier: 4.093A pdb=" N GLU S 102 " --> pdb=" O ASN S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 126 Processing helix chain 'S' and resid 139 through 151 Processing helix chain 'S' and resid 195 through 198 Processing helix chain 'S' and resid 334 through 354 removed outlier: 4.108A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS S 352 " --> pdb=" O GLN S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 373 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.796A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 528 removed outlier: 4.472A pdb=" N GLY T 527 " --> pdb=" O GLY T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.556A pdb=" N GLN T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 596 Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 660 removed outlier: 3.531A pdb=" N GLN T 658 " --> pdb=" O GLU T 654 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 Processing sheet with id=1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.815A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.900A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.423A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 393 through 394 removed outlier: 6.531A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.607A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.942A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.752A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=10, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.267A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=12, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.089A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.846A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.551A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.551A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=17, first strand: chain 'I' and resid 494 through 498 Processing sheet with id=18, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.815A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'I' and resid 75 through 76 removed outlier: 6.900A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=21, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=22, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.423A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'I' and resid 393 through 394 removed outlier: 6.530A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.607A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 259 through 261 removed outlier: 3.752A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'I' and resid 271 through 274 Processing sheet with id=26, first strand: chain 'I' and resid 315 through 323A removed outlier: 6.268A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN I 301 " --> pdb=" O ILE I 323 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=28, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.089A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.847A pdb=" N CYS K 92 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP K 103 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.551A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.551A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=33, first strand: chain 'S' and resid 494 through 498 Processing sheet with id=34, first strand: chain 'S' and resid 45 through 47 removed outlier: 3.815A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'S' and resid 75 through 76 removed outlier: 6.900A pdb=" N CYS S 54 " --> pdb=" O VAL S 75 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'S' and resid 91 through 94 Processing sheet with id=37, first strand: chain 'S' and resid 169 through 177 Processing sheet with id=38, first strand: chain 'S' and resid 200 through 203 removed outlier: 6.424A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR S 202 " --> pdb=" O TYR S 435 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'S' and resid 393 through 394 removed outlier: 6.531A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE S 443 " --> pdb=" O ARG S 298 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.607A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 10.881A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'S' and resid 259 through 261 removed outlier: 3.752A pdb=" N GLY S 451 " --> pdb=" O LEU S 260 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'S' and resid 271 through 274 Processing sheet with id=42, first strand: chain 'S' and resid 315 through 323A removed outlier: 6.267A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN S 301 " --> pdb=" O ILE S 323 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'U' and resid 3 through 8 Processing sheet with id=44, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.089A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.846A pdb=" N CYS U 92 " --> pdb=" O TRP U 103 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP U 103 " --> pdb=" O CYS U 92 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR U 94 " --> pdb=" O ASP U 101 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.551A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP V 35 " --> pdb=" O MET V 47 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.551A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'V' and resid 19 through 24 753 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.17 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3539 1.31 - 1.44: 5489 1.44 - 1.57: 10739 1.57 - 1.70: 33 1.70 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG 0 2 " pdb=" O5 NAG 0 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.81e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 23975 2.56 - 5.12: 2763 5.12 - 7.68: 325 7.68 - 10.24: 27 10.24 - 12.80: 3 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 123.50 -12.80 1.22e+00 6.72e-01 1.10e+02 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 123.50 -12.80 1.22e+00 6.72e-01 1.10e+02 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 123.47 -12.77 1.22e+00 6.72e-01 1.10e+02 angle pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 123.16 114.73 8.43 1.06e+00 8.90e-01 6.33e+01 angle pdb=" C ASP M 50 " pdb=" N VAL M 51 " pdb=" CA VAL M 51 " ideal model delta sigma weight residual 123.16 114.73 8.43 1.06e+00 8.90e-01 6.32e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 10842 17.56 - 35.12: 255 35.12 - 52.69: 78 52.69 - 70.25: 33 70.25 - 87.81: 15 Dihedral angle restraints: 11223 sinusoidal: 4476 harmonic: 6747 Sorted by residual: dihedral pdb=" CB CYS S 228 " pdb=" SG CYS S 228 " pdb=" SG CYS S 239 " pdb=" CB CYS S 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 11220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2392 0.102 - 0.203: 747 0.203 - 0.305: 119 0.305 - 0.406: 15 0.406 - 0.508: 6 Chirality restraints: 3279 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.56e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.56e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.53e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " 0.309 2.00e-02 2.50e+03 2.61e-01 8.51e+02 pdb=" C7 NAG J 702 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " -0.449 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " -0.309 2.00e-02 2.50e+03 2.61e-01 8.50e+02 pdb=" C7 NAG B 702 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " 0.449 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " -0.309 2.00e-02 2.50e+03 2.61e-01 8.48e+02 pdb=" C7 NAG T 702 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " 0.448 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.032 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2526 2.72 - 3.26: 17362 3.26 - 3.81: 31341 3.81 - 4.35: 39033 4.35 - 4.90: 65334 Nonbonded interactions: 155596 Sorted by model distance: nonbonded pdb=" O3 NAG B 702 " pdb=" O7 NAG B 702 " model vdw 2.174 3.040 nonbonded pdb=" O3 NAG J 702 " pdb=" O7 NAG J 702 " model vdw 2.175 3.040 nonbonded pdb=" O3 NAG T 702 " pdb=" O7 NAG T 702 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.237 3.040 ... (remaining 155591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 20.780 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.162 20097 Z= 1.279 Angle : 1.713 12.797 27426 Z= 1.105 Chirality : 0.099 0.508 3279 Planarity : 0.013 0.261 3339 Dihedral : 9.785 87.811 6783 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.26 % Favored : 96.48 % Rotamer: Outliers : 0.15 % Allowed : 0.29 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2304 helix: -0.32 (0.24), residues: 387 sheet: 0.76 (0.20), residues: 645 loop : 0.37 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 66 TYR 0.049 0.007 TYR V 36 PHE 0.036 0.006 PHE S 383 TRP 0.071 0.010 TRP S 427 HIS 0.007 0.002 HIS I 216 Details of bonding type rmsd/Z covalent geometry : bond 0.02449 / 1.28 (19974) covalent geometry : angle 1.68783 / 1.10 (27093) SS BOND : bond 0.04067 / 2.88 ( 36) SS BOND : angle 2.64047 / 1.85 ( 72) hydrogen bonds : bond 0.15905 / 10.58 ( 732) hydrogen bonds : angle 7.00409 / 4.93 ( 1926) link_ALPHA1-3 : bond 0.03310 / 1.66 ( 3) link_ALPHA1-3 : angle 2.27500 / 1.51 ( 9) link_BETA1-4 : bond 0.02599 / 1.48 ( 18) link_BETA1-4 : angle 3.68499 / 2.79 ( 54) link_NAG-ASN : bond 0.03221 / 1.89 ( 66) link_NAG-ASN : angle 3.20199 / 2.24 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 478 time to evaluate : 0.739 Fit side-chains REVERT: A 104 MET cc_start: 0.9051 (ttt) cc_final: 0.8760 (ttt) REVERT: A 502 LYS cc_start: 0.6674 (mmtp) cc_final: 0.6241 (mmtt) REVERT: I 502 LYS cc_start: 0.6590 (mmtp) cc_final: 0.5679 (mmtt) REVERT: M 47 MET cc_start: 0.8342 (mmm) cc_final: 0.7927 (mmp) REVERT: S 326 ILE cc_start: 0.8587 (mm) cc_final: 0.8349 (mt) REVERT: S 502 LYS cc_start: 0.6881 (mmtp) cc_final: 0.6107 (mmtt) outliers start: 3 outliers final: 0 residues processed: 481 average time/residue: 0.1686 time to fit residues: 119.5220 Evaluate side-chains 237 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN B 607 ASN L 39 HIS J 607 ASN J 630 GLN T 577 GLN V 39 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098297 restraints weight = 28861.000| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.27 r_work: 0.2952 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20097 Z= 0.165 Angle : 0.717 9.189 27426 Z= 0.366 Chirality : 0.046 0.226 3279 Planarity : 0.004 0.039 3339 Dihedral : 5.162 25.526 2520 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.17 % Favored : 96.57 % Rotamer: Outliers : 2.10 % Allowed : 6.70 % Favored : 91.20 % 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: 0.69 (0.17), residues: 2304 helix: 1.53 (0.27), residues: 384 sheet: 0.60 (0.20), residues: 648 loop : 0.14 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 444 TYR 0.015 0.002 TYR A 173 PHE 0.020 0.002 PHE A 383 TRP 0.015 0.001 TRP A 479 HIS 0.005 0.001 HIS U 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (19974) covalent geometry : angle 0.67467 / 0.36 (27093) SS BOND : bond 0.00268 / 0.17 ( 36) SS BOND : angle 0.92238 / 0.62 ( 72) hydrogen bonds : bond 0.05426 / 3.73 ( 732) hydrogen bonds : angle 5.55527 / 3.93 ( 1926) link_ALPHA1-3 : bond 0.00565 / 0.28 ( 3) link_ALPHA1-3 : angle 1.78025 / 1.10 ( 9) link_BETA1-4 : bond 0.00629 / 0.40 ( 18) link_BETA1-4 : angle 1.97738 / 1.44 ( 54) link_NAG-ASN : bond 0.00358 / 0.20 ( 66) link_NAG-ASN : angle 2.71457 / 1.91 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9335 (ttt) cc_final: 0.9057 (ttt) REVERT: A 150 MET cc_start: 0.8575 (mmp) cc_final: 0.8207 (mmp) REVERT: A 502 LYS cc_start: 0.6463 (mmtp) cc_final: 0.6202 (mmtt) REVERT: L 33 VAL cc_start: 0.8991 (t) cc_final: 0.8760 (m) REVERT: I 164 GLU cc_start: 0.8181 (mp0) cc_final: 0.7881 (mp0) REVERT: I 213 ILE cc_start: 0.8801 (mt) cc_final: 0.8559 (tt) REVERT: I 358 ILE cc_start: 0.8300 (mt) cc_final: 0.8010 (mp) REVERT: I 502 LYS cc_start: 0.6629 (mmtp) cc_final: 0.5448 (mmtm) REVERT: K 101 ASP cc_start: 0.8499 (m-30) cc_final: 0.8246 (m-30) REVERT: M 47 MET cc_start: 0.8869 (mmm) cc_final: 0.8560 (mmt) REVERT: M 58 VAL cc_start: 0.8137 (t) cc_final: 0.7901 (p) REVERT: S 502 LYS cc_start: 0.7133 (mmtp) cc_final: 0.6332 (mmtm) REVERT: U 13 GLN cc_start: 0.7831 (pm20) cc_final: 0.7594 (tt0) REVERT: U 52 ASP cc_start: 0.8694 (p0) cc_final: 0.8418 (p0) REVERT: U 64 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8235 (tttt) outliers start: 43 outliers final: 28 residues processed: 317 average time/residue: 0.1424 time to fit residues: 70.6063 Evaluate side-chains 260 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 607 ASN Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 82 HIS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 620 SER Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 85 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN A 302 ASN B 577 GLN I 374 HIS I 377 ASN S 302 ASN U 82AHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.093263 restraints weight = 29045.504| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.27 r_work: 0.2866 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20097 Z= 0.200 Angle : 0.676 11.119 27426 Z= 0.341 Chirality : 0.046 0.198 3279 Planarity : 0.004 0.035 3339 Dihedral : 5.063 28.677 2520 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.65 % Favored : 96.09 % Rotamer: Outliers : 2.15 % Allowed : 8.85 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.47 (0.18), residues: 2304 helix: 1.77 (0.28), residues: 381 sheet: 0.42 (0.20), residues: 675 loop : -0.14 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 71 TYR 0.013 0.002 TYR K 90 PHE 0.020 0.002 PHE I 383 TRP 0.012 0.001 TRP A 35 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (19974) covalent geometry : angle 0.64016 / 0.33 (27093) SS BOND : bond 0.00381 / 0.24 ( 36) SS BOND : angle 0.99498 / 0.72 ( 72) hydrogen bonds : bond 0.05135 / 3.53 ( 732) hydrogen bonds : angle 5.15252 / 3.65 ( 1926) link_ALPHA1-3 : bond 0.00699 / 0.35 ( 3) link_ALPHA1-3 : angle 1.24869 / 0.76 ( 9) link_BETA1-4 : bond 0.00357 / 0.21 ( 18) link_BETA1-4 : angle 1.52730 / 1.12 ( 54) link_NAG-ASN : bond 0.00488 / 0.27 ( 66) link_NAG-ASN : angle 2.49206 / 1.81 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9313 (ttt) cc_final: 0.9077 (ttt) REVERT: A 502 LYS cc_start: 0.6970 (mmtp) cc_final: 0.6025 (mmtm) REVERT: L 33 VAL cc_start: 0.9035 (t) cc_final: 0.8775 (m) REVERT: I 136 ASN cc_start: 0.8010 (m-40) cc_final: 0.7719 (t0) REVERT: I 164 GLU cc_start: 0.8402 (mp0) cc_final: 0.8146 (mp0) REVERT: I 213 ILE cc_start: 0.8960 (mt) cc_final: 0.8718 (tt) REVERT: I 358 ILE cc_start: 0.8492 (mt) cc_final: 0.8220 (mp) REVERT: I 502 LYS cc_start: 0.6894 (mmtp) cc_final: 0.5752 (mmtm) REVERT: M 47 MET cc_start: 0.8922 (mmm) cc_final: 0.8715 (mmt) REVERT: S 151 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7574 (ttm110) REVERT: S 326 ILE cc_start: 0.8794 (mm) cc_final: 0.8540 (mt) REVERT: S 395 TRP cc_start: 0.6926 (m-10) cc_final: 0.6675 (m-10) REVERT: S 502 LYS cc_start: 0.7413 (mmtp) cc_final: 0.6561 (mmtt) outliers start: 44 outliers final: 31 residues processed: 276 average time/residue: 0.1556 time to fit residues: 65.4060 Evaluate side-chains 250 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 574 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 620 SER Chi-restraints excluded: chain T residue 649 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 159 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN B 607 ASN H 73 ASN S 374 HIS T 607 ASN V 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.090018 restraints weight = 28936.730| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.28 r_work: 0.2816 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20097 Z= 0.241 Angle : 0.684 9.706 27426 Z= 0.345 Chirality : 0.047 0.245 3279 Planarity : 0.004 0.039 3339 Dihedral : 5.133 31.352 2520 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.08 % Favored : 95.70 % Rotamer: Outliers : 2.49 % Allowed : 9.78 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2304 helix: 1.41 (0.27), residues: 390 sheet: 0.32 (0.19), residues: 705 loop : -0.48 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 480 TYR 0.021 0.002 TYR K 90 PHE 0.022 0.002 PHE I 383 TRP 0.016 0.002 TRP K 103 HIS 0.004 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (19974) covalent geometry : angle 0.65281 / 0.34 (27093) SS BOND : bond 0.00616 / 0.40 ( 36) SS BOND : angle 1.23788 / 0.97 ( 72) hydrogen bonds : bond 0.05309 / 3.67 ( 732) hydrogen bonds : angle 5.08353 / 3.60 ( 1926) link_ALPHA1-3 : bond 0.00462 / 0.23 ( 3) link_ALPHA1-3 : angle 1.40956 / 0.86 ( 9) link_BETA1-4 : bond 0.00298 / 0.19 ( 18) link_BETA1-4 : angle 1.47540 / 1.10 ( 54) link_NAG-ASN : bond 0.00495 / 0.29 ( 66) link_NAG-ASN : angle 2.28642 / 1.63 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7444 (ttm110) REVERT: A 502 LYS cc_start: 0.7094 (mmtp) cc_final: 0.6029 (mmtm) REVERT: I 136 ASN cc_start: 0.7978 (m-40) cc_final: 0.7733 (t0) REVERT: I 502 LYS cc_start: 0.6950 (mmtp) cc_final: 0.6217 (mmtt) REVERT: K 100 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8947 (mp) REVERT: M 95 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: S 211 GLU cc_start: 0.8311 (mp0) cc_final: 0.8003 (mp0) REVERT: S 502 LYS cc_start: 0.7436 (mmtp) cc_final: 0.6630 (mmtt) REVERT: T 657 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8767 (mm-30) outliers start: 51 outliers final: 39 residues processed: 279 average time/residue: 0.1396 time to fit residues: 59.9239 Evaluate side-chains 265 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 620 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 135 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 228 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 175 optimal weight: 0.0970 chunk 30 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN T 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.093437 restraints weight = 28660.376| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.24 r_work: 0.2872 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20097 Z= 0.108 Angle : 0.571 11.136 27426 Z= 0.288 Chirality : 0.043 0.194 3279 Planarity : 0.004 0.040 3339 Dihedral : 4.832 33.081 2520 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 1.52 % Allowed : 11.63 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2304 helix: 2.01 (0.27), residues: 381 sheet: 0.32 (0.19), residues: 747 loop : -0.38 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 151 TYR 0.018 0.001 TYR K 90 PHE 0.016 0.001 PHE A 53 TRP 0.008 0.001 TRP A 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (19974) covalent geometry : angle 0.54230 / 0.28 (27093) SS BOND : bond 0.00287 / 0.16 ( 36) SS BOND : angle 0.69821 / 0.55 ( 72) hydrogen bonds : bond 0.04156 / 2.87 ( 732) hydrogen bonds : angle 4.77124 / 3.37 ( 1926) link_ALPHA1-3 : bond 0.00489 / 0.25 ( 3) link_ALPHA1-3 : angle 1.42306 / 0.87 ( 9) link_BETA1-4 : bond 0.00361 / 0.21 ( 18) link_BETA1-4 : angle 1.24145 / 0.93 ( 54) link_NAG-ASN : bond 0.00300 / 0.16 ( 66) link_NAG-ASN : angle 2.05508 / 1.45 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8883 (m) REVERT: A 502 LYS cc_start: 0.6794 (mmtp) cc_final: 0.6438 (mmtt) REVERT: I 136 ASN cc_start: 0.7966 (m-40) cc_final: 0.7708 (t0) REVERT: I 217 TYR cc_start: 0.8916 (m-80) cc_final: 0.7886 (m-80) REVERT: I 502 LYS cc_start: 0.6806 (mmtp) cc_final: 0.5800 (mmtm) REVERT: M 58 VAL cc_start: 0.8189 (p) cc_final: 0.7966 (t) REVERT: S 211 GLU cc_start: 0.8274 (mp0) cc_final: 0.8011 (mp0) REVERT: S 326 ILE cc_start: 0.8820 (mm) cc_final: 0.8599 (mt) REVERT: S 502 LYS cc_start: 0.7208 (mmtp) cc_final: 0.6336 (mmtt) REVERT: T 657 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8723 (mm-30) REVERT: V 33 VAL cc_start: 0.9058 (t) cc_final: 0.8820 (m) outliers start: 31 outliers final: 23 residues processed: 258 average time/residue: 0.1523 time to fit residues: 59.7963 Evaluate side-chains 243 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN B 607 ASN K 39 GLN M 38 GLN T 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.091455 restraints weight = 28767.664| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.27 r_work: 0.2846 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20097 Z= 0.163 Angle : 0.599 9.132 27426 Z= 0.300 Chirality : 0.045 0.268 3279 Planarity : 0.004 0.042 3339 Dihedral : 4.791 27.770 2520 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.83 % Rotamer: Outliers : 2.05 % Allowed : 11.19 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2304 helix: 2.00 (0.27), residues: 381 sheet: 0.31 (0.19), residues: 741 loop : -0.43 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 151 TYR 0.016 0.001 TYR K 90 PHE 0.028 0.002 PHE H 67 TRP 0.009 0.001 TRP H 103 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (19974) covalent geometry : angle 0.56670 / 0.29 (27093) SS BOND : bond 0.00354 / 0.20 ( 36) SS BOND : angle 0.82511 / 0.63 ( 72) hydrogen bonds : bond 0.04472 / 3.09 ( 732) hydrogen bonds : angle 4.75037 / 3.36 ( 1926) link_ALPHA1-3 : bond 0.00483 / 0.24 ( 3) link_ALPHA1-3 : angle 1.38513 / 0.84 ( 9) link_BETA1-4 : bond 0.00334 / 0.21 ( 18) link_BETA1-4 : angle 1.31792 / 0.98 ( 54) link_NAG-ASN : bond 0.00366 / 0.20 ( 66) link_NAG-ASN : angle 2.22123 / 1.69 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 502 LYS cc_start: 0.6993 (mmtp) cc_final: 0.5727 (mmtm) REVERT: H 100 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9081 (mp) REVERT: L 95 GLN cc_start: 0.8340 (pt0) cc_final: 0.8086 (pt0) REVERT: I 136 ASN cc_start: 0.8021 (m-40) cc_final: 0.7737 (t0) REVERT: I 502 LYS cc_start: 0.7051 (mmtp) cc_final: 0.6365 (mmtt) REVERT: K 100 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8931 (mp) REVERT: S 211 GLU cc_start: 0.8302 (mp0) cc_final: 0.8043 (mp0) REVERT: S 502 LYS cc_start: 0.7228 (mmtp) cc_final: 0.6242 (mmtt) REVERT: T 657 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8766 (mm-30) REVERT: U 100 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8935 (mp) outliers start: 42 outliers final: 34 residues processed: 250 average time/residue: 0.1527 time to fit residues: 58.2886 Evaluate side-chains 245 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 607 ASN Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 65 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN B 607 ASN T 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.089120 restraints weight = 28861.115| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.58 r_work: 0.2763 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20097 Z= 0.187 Angle : 0.615 8.987 27426 Z= 0.309 Chirality : 0.045 0.254 3279 Planarity : 0.004 0.042 3339 Dihedral : 4.834 23.680 2520 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 2.44 % Allowed : 10.80 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 2304 helix: 1.65 (0.27), residues: 387 sheet: 0.25 (0.19), residues: 741 loop : -0.53 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 151 TYR 0.023 0.001 TYR K 90 PHE 0.019 0.002 PHE U 67 TRP 0.011 0.001 TRP H 103 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (19974) covalent geometry : angle 0.58727 / 0.30 (27093) SS BOND : bond 0.00395 / 0.22 ( 36) SS BOND : angle 0.87690 / 0.67 ( 72) hydrogen bonds : bond 0.04717 / 3.26 ( 732) hydrogen bonds : angle 4.78622 / 3.39 ( 1926) link_ALPHA1-3 : bond 0.00474 / 0.24 ( 3) link_ALPHA1-3 : angle 1.39691 / 0.85 ( 9) link_BETA1-4 : bond 0.00314 / 0.19 ( 18) link_BETA1-4 : angle 1.36404 / 1.01 ( 54) link_NAG-ASN : bond 0.00392 / 0.22 ( 66) link_NAG-ASN : angle 2.08597 / 1.52 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 502 LYS cc_start: 0.7068 (mmtp) cc_final: 0.6155 (mmtt) REVERT: H 100 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9133 (mp) REVERT: L 95 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: I 136 ASN cc_start: 0.8058 (m-40) cc_final: 0.7752 (t0) REVERT: I 428 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8440 (mm110) REVERT: I 502 LYS cc_start: 0.7102 (mmtp) cc_final: 0.6537 (mmtt) REVERT: J 620 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.9081 (p) REVERT: K 100 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9015 (mp) REVERT: S 211 GLU cc_start: 0.8402 (mp0) cc_final: 0.8009 (mp0) REVERT: S 308 ARG cc_start: 0.9120 (mtp85) cc_final: 0.8873 (mtp180) REVERT: S 502 LYS cc_start: 0.7362 (mmtp) cc_final: 0.6375 (mmtt) REVERT: T 657 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8748 (mm-30) REVERT: U 100 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8978 (mp) outliers start: 50 outliers final: 39 residues processed: 262 average time/residue: 0.1542 time to fit residues: 61.7053 Evaluate side-chains 256 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 35 TRP Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 125 optimal weight: 0.0020 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS B 577 GLN B 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.088309 restraints weight = 28821.062| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.56 r_work: 0.2742 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20097 Z= 0.220 Angle : 0.639 10.400 27426 Z= 0.319 Chirality : 0.046 0.212 3279 Planarity : 0.004 0.042 3339 Dihedral : 4.892 22.859 2520 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 2.44 % Allowed : 11.09 % Favored : 86.46 % 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: 0.00 (0.18), residues: 2304 helix: 1.53 (0.27), residues: 387 sheet: 0.21 (0.19), residues: 741 loop : -0.61 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 151 TYR 0.020 0.002 TYR K 90 PHE 0.044 0.002 PHE H 67 TRP 0.011 0.002 TRP A 427 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (19974) covalent geometry : angle 0.61073 / 0.31 (27093) SS BOND : bond 0.00437 / 0.25 ( 36) SS BOND : angle 1.02897 / 0.78 ( 72) hydrogen bonds : bond 0.04886 / 3.37 ( 732) hydrogen bonds : angle 4.85139 / 3.44 ( 1926) link_ALPHA1-3 : bond 0.00460 / 0.23 ( 3) link_ALPHA1-3 : angle 1.39624 / 0.85 ( 9) link_BETA1-4 : bond 0.00324 / 0.20 ( 18) link_BETA1-4 : angle 1.40345 / 1.04 ( 54) link_NAG-ASN : bond 0.00418 / 0.25 ( 66) link_NAG-ASN : angle 2.11767 / 1.53 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7323 (ttm110) REVERT: A 502 LYS cc_start: 0.7096 (mmtp) cc_final: 0.6137 (mmtt) REVERT: H 100 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9126 (mp) REVERT: I 136 ASN cc_start: 0.8093 (m-40) cc_final: 0.7791 (t0) REVERT: I 428 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8461 (mm110) REVERT: I 502 LYS cc_start: 0.7157 (mmtp) cc_final: 0.6548 (mmtt) REVERT: J 620 SER cc_start: 0.9304 (OUTLIER) cc_final: 0.9090 (p) REVERT: K 100 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9038 (mp) REVERT: S 211 GLU cc_start: 0.8375 (mp0) cc_final: 0.7986 (mp0) REVERT: S 308 ARG cc_start: 0.9124 (mtp85) cc_final: 0.8907 (mtp180) REVERT: S 502 LYS cc_start: 0.7392 (mmtp) cc_final: 0.6822 (mmtt) REVERT: T 657 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8758 (mm-30) REVERT: U 100 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9013 (mp) outliers start: 50 outliers final: 42 residues processed: 250 average time/residue: 0.1458 time to fit residues: 55.6469 Evaluate side-chains 259 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 35 TRP Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN B 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.090086 restraints weight = 28568.449| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.57 r_work: 0.2773 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20097 Z= 0.139 Angle : 0.579 10.678 27426 Z= 0.291 Chirality : 0.044 0.185 3279 Planarity : 0.004 0.042 3339 Dihedral : 4.747 21.295 2520 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.49 % Rotamer: Outliers : 2.15 % Allowed : 11.24 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2304 helix: 1.93 (0.27), residues: 378 sheet: 0.25 (0.19), residues: 741 loop : -0.52 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 151 TYR 0.019 0.001 TYR K 90 PHE 0.027 0.001 PHE H 67 TRP 0.009 0.001 TRP A 427 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (19974) covalent geometry : angle 0.55212 / 0.29 (27093) SS BOND : bond 0.00353 / 0.19 ( 36) SS BOND : angle 0.73958 / 0.58 ( 72) hydrogen bonds : bond 0.04290 / 2.96 ( 732) hydrogen bonds : angle 4.72588 / 3.34 ( 1926) link_ALPHA1-3 : bond 0.00461 / 0.23 ( 3) link_ALPHA1-3 : angle 1.40843 / 0.86 ( 9) link_BETA1-4 : bond 0.00342 / 0.21 ( 18) link_BETA1-4 : angle 1.28617 / 0.95 ( 54) link_NAG-ASN : bond 0.00292 / 0.16 ( 66) link_NAG-ASN : angle 1.99712 / 1.43 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7314 (ttm110) REVERT: A 502 LYS cc_start: 0.6888 (mmtp) cc_final: 0.6438 (mmtt) REVERT: I 136 ASN cc_start: 0.8074 (m-40) cc_final: 0.7786 (t0) REVERT: I 217 TYR cc_start: 0.9031 (m-80) cc_final: 0.7985 (m-80) REVERT: I 428 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8445 (mm110) REVERT: I 502 LYS cc_start: 0.6958 (mmtp) cc_final: 0.6320 (mmtt) REVERT: K 100 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9063 (mp) REVERT: S 211 GLU cc_start: 0.8352 (mp0) cc_final: 0.7952 (mp0) REVERT: S 308 ARG cc_start: 0.9104 (mtp85) cc_final: 0.8871 (mtp180) REVERT: S 502 LYS cc_start: 0.7251 (mmtp) cc_final: 0.6799 (mmtt) REVERT: T 657 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8739 (mm-30) outliers start: 44 outliers final: 35 residues processed: 256 average time/residue: 0.1451 time to fit residues: 57.0262 Evaluate side-chains 255 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 218 optimal weight: 0.0570 chunk 196 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN T 651 ASN U 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.089397 restraints weight = 28941.170| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.58 r_work: 0.2761 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20097 Z= 0.169 Angle : 0.605 12.077 27426 Z= 0.302 Chirality : 0.045 0.193 3279 Planarity : 0.004 0.043 3339 Dihedral : 4.746 21.864 2520 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.60 % Favored : 95.27 % Rotamer: Outliers : 1.91 % Allowed : 11.53 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2304 helix: 1.93 (0.27), residues: 378 sheet: 0.22 (0.19), residues: 741 loop : -0.54 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 151 TYR 0.024 0.001 TYR V 49 PHE 0.018 0.002 PHE H 67 TRP 0.010 0.001 TRP H 103 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (19974) covalent geometry : angle 0.57940 / 0.30 (27093) SS BOND : bond 0.00383 / 0.21 ( 36) SS BOND : angle 0.85822 / 0.66 ( 72) hydrogen bonds : bond 0.04500 / 3.10 ( 732) hydrogen bonds : angle 4.75467 / 3.36 ( 1926) link_ALPHA1-3 : bond 0.00467 / 0.23 ( 3) link_ALPHA1-3 : angle 1.38816 / 0.84 ( 9) link_BETA1-4 : bond 0.00330 / 0.20 ( 18) link_BETA1-4 : angle 1.33374 / 0.98 ( 54) link_NAG-ASN : bond 0.00335 / 0.19 ( 66) link_NAG-ASN : angle 1.99106 / 1.42 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7334 (ttm110) REVERT: A 502 LYS cc_start: 0.7094 (mmtp) cc_final: 0.6572 (mmtt) REVERT: L 95 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: I 136 ASN cc_start: 0.8099 (m-40) cc_final: 0.7816 (t0) REVERT: I 217 TYR cc_start: 0.9035 (m-80) cc_final: 0.7988 (m-80) REVERT: I 428 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8452 (mm110) REVERT: I 502 LYS cc_start: 0.7077 (mmtp) cc_final: 0.6420 (mmtt) REVERT: K 100 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9021 (mp) REVERT: S 136 ASN cc_start: 0.7831 (m-40) cc_final: 0.7609 (t0) REVERT: S 211 GLU cc_start: 0.8424 (mp0) cc_final: 0.8020 (mp0) REVERT: S 308 ARG cc_start: 0.9135 (mtp85) cc_final: 0.8928 (mtp180) REVERT: S 502 LYS cc_start: 0.7186 (mmtp) cc_final: 0.5707 (mmtm) REVERT: T 657 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8779 (mm-30) outliers start: 39 outliers final: 37 residues processed: 247 average time/residue: 0.1499 time to fit residues: 56.0878 Evaluate side-chains 257 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 35 TRP Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 27 optimal weight: 4.9990 chunk 223 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 577 GLN U 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.089889 restraints weight = 28827.679| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.57 r_work: 0.2768 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20097 Z= 0.155 Angle : 0.585 10.402 27426 Z= 0.294 Chirality : 0.044 0.191 3279 Planarity : 0.004 0.043 3339 Dihedral : 4.688 20.817 2520 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.47 % Favored : 95.40 % Rotamer: Outliers : 1.96 % Allowed : 11.63 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2304 helix: 1.99 (0.27), residues: 378 sheet: 0.28 (0.19), residues: 726 loop : -0.55 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 151 TYR 0.024 0.001 TYR V 49 PHE 0.019 0.001 PHE H 67 TRP 0.011 0.001 TRP S 395 HIS 0.004 0.001 HIS U 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (19974) covalent geometry : angle 0.55998 / 0.29 (27093) SS BOND : bond 0.00368 / 0.20 ( 36) SS BOND : angle 0.77006 / 0.60 ( 72) hydrogen bonds : bond 0.04325 / 2.99 ( 732) hydrogen bonds : angle 4.71633 / 3.34 ( 1926) link_ALPHA1-3 : bond 0.00459 / 0.23 ( 3) link_ALPHA1-3 : angle 1.39817 / 0.85 ( 9) link_BETA1-4 : bond 0.00337 / 0.21 ( 18) link_BETA1-4 : angle 1.29190 / 0.95 ( 54) link_NAG-ASN : bond 0.00298 / 0.17 ( 66) link_NAG-ASN : angle 1.94009 / 1.38 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5123.86 seconds wall clock time: 88 minutes 34.39 seconds (5314.39 seconds total)