Starting phenix.real_space_refine on Sat Sep 28 17:05:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9u_22111/09_2024/6x9u_22111.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9u_22111/09_2024/6x9u_22111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9u_22111/09_2024/6x9u_22111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9u_22111/09_2024/6x9u_22111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9u_22111/09_2024/6x9u_22111.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9u_22111/09_2024/6x9u_22111.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19590 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "T" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "U" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "V" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "T" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 11.80, per 1000 atoms: 0.60 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: 5.67 Conformation dependent library (CDL) restraints added in 2.4 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: 2.97 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: 7.82 Time building geometry restraints manager: 6.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3539 1.31 - 1.44: 5489 1.44 - 1.57: 10739 1.57 - 1.70: 33 1.70 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG 0 2 " pdb=" O5 NAG 0 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.81e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 23975 2.56 - 5.12: 2763 5.12 - 7.68: 325 7.68 - 10.24: 27 10.24 - 12.80: 3 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 123.50 -12.80 1.22e+00 6.72e-01 1.10e+02 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 123.50 -12.80 1.22e+00 6.72e-01 1.10e+02 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 123.47 -12.77 1.22e+00 6.72e-01 1.10e+02 angle pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 123.16 114.73 8.43 1.06e+00 8.90e-01 6.33e+01 angle pdb=" C ASP M 50 " pdb=" N VAL M 51 " pdb=" CA VAL M 51 " ideal model delta sigma weight residual 123.16 114.73 8.43 1.06e+00 8.90e-01 6.32e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 12609 21.83 - 43.66: 282 43.66 - 65.48: 102 65.48 - 87.31: 30 87.31 - 109.14: 15 Dihedral angle restraints: 13038 sinusoidal: 6291 harmonic: 6747 Sorted by residual: dihedral pdb=" CB CYS S 228 " pdb=" SG CYS S 228 " pdb=" SG CYS S 239 " pdb=" CB CYS S 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 13035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2392 0.102 - 0.203: 747 0.203 - 0.305: 119 0.305 - 0.406: 15 0.406 - 0.508: 6 Chirality restraints: 3279 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.56e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.56e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.53e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " 0.309 2.00e-02 2.50e+03 2.61e-01 8.51e+02 pdb=" C7 NAG J 702 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " -0.449 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " -0.309 2.00e-02 2.50e+03 2.61e-01 8.50e+02 pdb=" C7 NAG B 702 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " 0.449 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " -0.309 2.00e-02 2.50e+03 2.61e-01 8.48e+02 pdb=" C7 NAG T 702 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " 0.448 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.032 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2526 2.72 - 3.26: 17362 3.26 - 3.81: 31341 3.81 - 4.35: 39033 4.35 - 4.90: 65334 Nonbonded interactions: 155596 Sorted by model distance: nonbonded pdb=" O3 NAG B 702 " pdb=" O7 NAG B 702 " model vdw 2.174 3.040 nonbonded pdb=" O3 NAG J 702 " pdb=" O7 NAG J 702 " model vdw 2.175 3.040 nonbonded pdb=" O3 NAG T 702 " pdb=" O7 NAG T 702 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.237 3.040 ... (remaining 155591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.250 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: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.200 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.140 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.162 19974 Z= 1.579 Angle : 1.688 12.797 27093 Z= 1.105 Chirality : 0.099 0.508 3279 Planarity : 0.013 0.261 3339 Dihedral : 11.511 109.137 8598 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.26 % Favored : 96.48 % Rotamer: Outliers : 0.15 % Allowed : 0.29 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (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 TRP 0.071 0.010 TRP S 427 HIS 0.007 0.002 HIS I 216 PHE 0.036 0.006 PHE S 383 TYR 0.049 0.007 TYR V 36 ARG 0.008 0.001 ARG K 66 *********************** 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 fitting. rotamer outliers: 3 poor density : 478 time to evaluate : 2.133 Fit side-chains REVERT: A 104 MET cc_start: 0.9051 (ttt) cc_final: 0.8759 (ttt) REVERT: A 502 LYS cc_start: 0.6674 (mmtp) cc_final: 0.6158 (mmtt) REVERT: I 502 LYS cc_start: 0.6590 (mmtp) cc_final: 0.5678 (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: 0.3468 time to fit residues: 242.2835 Evaluate side-chains 236 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 607 ASN L 39 HIS J 607 ASN J 630 GLN T 577 GLN V 39 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19974 Z= 0.229 Angle : 0.676 10.224 27093 Z= 0.360 Chirality : 0.047 0.214 3279 Planarity : 0.004 0.033 3339 Dihedral : 8.454 67.149 4335 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.17 % Favored : 96.57 % Rotamer: Outliers : 1.96 % Allowed : 6.99 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2304 helix: 1.56 (0.27), residues: 384 sheet: 0.64 (0.20), residues: 648 loop : 0.17 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 479 HIS 0.005 0.001 HIS U 82A PHE 0.021 0.002 PHE A 383 TYR 0.014 0.002 TYR A 173 ARG 0.005 0.001 ARG S 444 *********************** 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 323 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 283 time to evaluate : 2.243 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8893 (ttt) cc_final: 0.8581 (ttt) REVERT: A 150 MET cc_start: 0.8425 (mmp) cc_final: 0.8011 (mmp) REVERT: A 502 LYS cc_start: 0.6405 (mmtp) cc_final: 0.6204 (mmtt) REVERT: I 502 LYS cc_start: 0.6558 (mmtp) cc_final: 0.5510 (mmtm) REVERT: S 502 LYS cc_start: 0.7113 (mmtp) cc_final: 0.6376 (mmtm) REVERT: U 52 ASP cc_start: 0.8601 (p0) cc_final: 0.8324 (p0) REVERT: U 64 LYS cc_start: 0.8273 (ttmm) cc_final: 0.8035 (tttt) outliers start: 40 outliers final: 28 residues processed: 314 average time/residue: 0.3021 time to fit residues: 146.2688 Evaluate side-chains 260 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 2.021 ------------------------------------------------------------------------------- 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 116 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 210 optimal weight: 0.6980 chunk 227 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 302 ASN B 577 GLN B 607 ASN I 67 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN J 607 ASN S 302 ASN U 82AHIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19974 Z= 0.289 Angle : 0.628 10.462 27093 Z= 0.328 Chirality : 0.046 0.175 3279 Planarity : 0.004 0.036 3339 Dihedral : 6.999 53.308 4335 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.73 % Favored : 96.01 % Rotamer: Outliers : 1.86 % Allowed : 9.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2304 helix: 1.82 (0.28), residues: 381 sheet: 0.56 (0.20), residues: 669 loop : -0.13 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.004 0.001 HIS S 105 PHE 0.019 0.002 PHE I 383 TYR 0.019 0.002 TYR K 90 ARG 0.005 0.000 ARG U 71 *********************** 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 278 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 240 time to evaluate : 2.425 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9073 (t) cc_final: 0.8862 (m) REVERT: A 104 MET cc_start: 0.8893 (ttt) cc_final: 0.8650 (ttt) REVERT: A 502 LYS cc_start: 0.6687 (mmtp) cc_final: 0.5846 (mmtm) REVERT: L 36 TYR cc_start: 0.8856 (m-80) cc_final: 0.8422 (m-80) REVERT: I 136 ASN cc_start: 0.7869 (m-40) cc_final: 0.7622 (t0) REVERT: I 217 TYR cc_start: 0.8577 (m-80) cc_final: 0.7915 (m-80) REVERT: I 502 LYS cc_start: 0.7042 (mmtp) cc_final: 0.5904 (mmtp) REVERT: S 326 ILE cc_start: 0.8873 (mm) cc_final: 0.8577 (mt) REVERT: S 502 LYS cc_start: 0.7300 (mmtp) cc_final: 0.6511 (mmtt) outliers start: 38 outliers final: 29 residues processed: 269 average time/residue: 0.3146 time to fit residues: 129.9843 Evaluate side-chains 250 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 221 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 574 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 620 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 210 optimal weight: 0.1980 chunk 223 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 607 ASN T 607 ASN V 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19974 Z= 0.209 Angle : 0.568 11.090 27093 Z= 0.296 Chirality : 0.044 0.209 3279 Planarity : 0.004 0.039 3339 Dihedral : 6.103 52.168 4335 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.47 % Favored : 96.27 % Rotamer: Outliers : 1.86 % Allowed : 9.68 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2304 helix: 1.97 (0.28), residues: 381 sheet: 0.42 (0.19), residues: 711 loop : -0.13 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 103 HIS 0.004 0.001 HIS S 105 PHE 0.017 0.002 PHE H 67 TYR 0.016 0.001 TYR K 90 ARG 0.004 0.000 ARG I 151 *********************** 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 282 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 244 time to evaluate : 2.282 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8879 (ttt) cc_final: 0.8656 (ttt) REVERT: A 502 LYS cc_start: 0.6747 (mmtp) cc_final: 0.6223 (mmtp) REVERT: L 36 TYR cc_start: 0.8848 (m-80) cc_final: 0.8401 (m-80) REVERT: I 136 ASN cc_start: 0.7917 (m-40) cc_final: 0.7663 (t0) REVERT: I 217 TYR cc_start: 0.8480 (m-80) cc_final: 0.7938 (m-80) REVERT: I 502 LYS cc_start: 0.6838 (mmtp) cc_final: 0.5850 (mmtm) REVERT: S 326 ILE cc_start: 0.8927 (mm) cc_final: 0.8684 (mt) REVERT: S 502 LYS cc_start: 0.7368 (mmtp) cc_final: 0.6686 (mmtt) outliers start: 38 outliers final: 32 residues processed: 273 average time/residue: 0.3156 time to fit residues: 132.0049 Evaluate side-chains 254 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 222 time to evaluate : 2.311 ------------------------------------------------------------------------------- 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 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 174 SER Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain 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 9 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 607 ASN Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain 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 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 185 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 200 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN I 374 HIS J 651 ASN S 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19974 Z= 0.327 Angle : 0.616 10.969 27093 Z= 0.319 Chirality : 0.046 0.199 3279 Planarity : 0.004 0.044 3339 Dihedral : 6.015 40.925 4335 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 2.00 % Allowed : 10.41 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2304 helix: 1.86 (0.28), residues: 381 sheet: 0.31 (0.19), residues: 747 loop : -0.31 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 103 HIS 0.004 0.001 HIS S 105 PHE 0.019 0.002 PHE H 67 TYR 0.015 0.002 TYR K 90 ARG 0.004 0.001 ARG I 151 *********************** 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 270 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 229 time to evaluate : 2.232 Fit side-chains revert: symmetry clash REVERT: A 502 LYS cc_start: 0.6937 (mmtp) cc_final: 0.6582 (mmtt) REVERT: I 136 ASN cc_start: 0.7895 (m-40) cc_final: 0.7667 (t0) REVERT: I 217 TYR cc_start: 0.8505 (m-80) cc_final: 0.7952 (m-80) REVERT: I 502 LYS cc_start: 0.7028 (mmtp) cc_final: 0.6355 (mmtt) REVERT: K 100 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8895 (mp) REVERT: S 326 ILE cc_start: 0.8952 (mm) cc_final: 0.8748 (mt) REVERT: S 502 LYS cc_start: 0.7238 (mmtp) cc_final: 0.6403 (mmtm) outliers start: 41 outliers final: 36 residues processed: 261 average time/residue: 0.3182 time to fit residues: 126.3374 Evaluate side-chains 255 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 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 174 SER 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 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain 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 20 LEU Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 577 GLN H 73 ASN J 577 GLN T 577 GLN T 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 19974 Z= 0.457 Angle : 0.692 10.132 27093 Z= 0.357 Chirality : 0.049 0.210 3279 Planarity : 0.005 0.046 3339 Dihedral : 6.653 48.605 4335 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.90 % Favored : 94.97 % Rotamer: Outliers : 2.79 % Allowed : 10.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2304 helix: 1.23 (0.27), residues: 393 sheet: 0.19 (0.19), residues: 717 loop : -0.67 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 103 HIS 0.004 0.001 HIS I 105 PHE 0.025 0.003 PHE A 383 TYR 0.020 0.002 TYR K 90 ARG 0.006 0.001 ARG S 480 *********************** 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 284 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 227 time to evaluate : 2.226 Fit side-chains revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7543 (ttm110) REVERT: A 502 LYS cc_start: 0.7064 (mmtp) cc_final: 0.6597 (mmtt) REVERT: I 136 ASN cc_start: 0.7955 (m-40) cc_final: 0.7709 (t0) REVERT: I 502 LYS cc_start: 0.6977 (mmtp) cc_final: 0.6586 (mmtt) REVERT: K 100 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9012 (mp) REVERT: S 502 LYS cc_start: 0.7308 (mmtp) cc_final: 0.6427 (mmtm) REVERT: U 67 PHE cc_start: 0.8405 (m-80) cc_final: 0.8150 (m-80) REVERT: U 100 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8823 (mp) outliers start: 57 outliers final: 44 residues processed: 270 average time/residue: 0.3242 time to fit residues: 133.7421 Evaluate side-chains 261 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 215 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain 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 174 SER Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 98 SER 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 26 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 620 SER Chi-restraints excluded: chain T residue 654 GLU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 20 LEU 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 5 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN J 577 GLN T 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19974 Z= 0.336 Angle : 0.619 9.650 27093 Z= 0.320 Chirality : 0.046 0.315 3279 Planarity : 0.004 0.043 3339 Dihedral : 6.488 52.425 4335 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.51 % Favored : 95.36 % Rotamer: Outliers : 2.44 % Allowed : 10.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2304 helix: 1.31 (0.27), residues: 387 sheet: 0.18 (0.19), residues: 705 loop : -0.72 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 427 HIS 0.004 0.001 HIS S 105 PHE 0.021 0.002 PHE U 67 TYR 0.014 0.002 TYR U 100G ARG 0.006 0.001 ARG I 151 *********************** 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 270 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 220 time to evaluate : 2.318 Fit side-chains revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7722 (ttm110) cc_final: 0.7522 (ttm110) REVERT: A 502 LYS cc_start: 0.7097 (mmtp) cc_final: 0.6607 (mmtt) REVERT: H 100 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9024 (mp) REVERT: I 136 ASN cc_start: 0.7946 (m-40) cc_final: 0.7690 (t0) REVERT: K 100 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9058 (mp) REVERT: S 502 LYS cc_start: 0.7323 (mmtp) cc_final: 0.6422 (mmtt) REVERT: U 67 PHE cc_start: 0.8444 (m-80) cc_final: 0.8235 (m-80) outliers start: 50 outliers final: 42 residues processed: 260 average time/residue: 0.3302 time to fit residues: 129.7731 Evaluate side-chains 256 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 212 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU 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 20 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 174 SER 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 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 98 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 SER 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 20 LEU Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain V residue 5 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN K 39 GLN M 38 GLN T 607 ASN U 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19974 Z= 0.146 Angle : 0.522 8.710 27093 Z= 0.274 Chirality : 0.043 0.257 3279 Planarity : 0.004 0.042 3339 Dihedral : 5.941 59.553 4335 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 1.81 % Allowed : 11.49 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2304 helix: 2.04 (0.27), residues: 378 sheet: 0.28 (0.19), residues: 741 loop : -0.57 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 571 HIS 0.003 0.001 HIS I 105 PHE 0.047 0.001 PHE K 67 TYR 0.015 0.001 TYR H 100G ARG 0.008 0.000 ARG S 151 *********************** 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 269 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 232 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7457 (ttm110) REVERT: A 502 LYS cc_start: 0.6814 (mmtp) cc_final: 0.6516 (mmtt) REVERT: I 217 TYR cc_start: 0.8425 (m-80) cc_final: 0.7911 (m-80) REVERT: I 502 LYS cc_start: 0.6949 (mmtt) cc_final: 0.6079 (mmtp) REVERT: S 502 LYS cc_start: 0.7146 (mmtp) cc_final: 0.6320 (mmtm) outliers start: 37 outliers final: 30 residues processed: 257 average time/residue: 0.3149 time to fit residues: 123.5988 Evaluate side-chains 244 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 174 SER 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 82 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 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 U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 26 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 206 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 651 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19974 Z= 0.187 Angle : 0.531 8.702 27093 Z= 0.278 Chirality : 0.043 0.216 3279 Planarity : 0.004 0.043 3339 Dihedral : 5.801 58.810 4335 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.57 % Rotamer: Outliers : 1.86 % Allowed : 11.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2304 helix: 2.16 (0.27), residues: 378 sheet: 0.31 (0.19), residues: 741 loop : -0.52 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 571 HIS 0.003 0.001 HIS I 105 PHE 0.033 0.002 PHE K 67 TYR 0.014 0.001 TYR M 49 ARG 0.006 0.000 ARG S 151 *********************** 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 260 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 222 time to evaluate : 2.752 Fit side-chains revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7451 (ttm110) REVERT: A 502 LYS cc_start: 0.6848 (mmtp) cc_final: 0.6539 (mmtt) REVERT: I 136 ASN cc_start: 0.7876 (t0) cc_final: 0.7634 (t0) REVERT: I 217 TYR cc_start: 0.8402 (m-80) cc_final: 0.7908 (m-80) REVERT: I 502 LYS cc_start: 0.7072 (mmtt) cc_final: 0.6142 (mmtm) REVERT: S 502 LYS cc_start: 0.7232 (mmtp) cc_final: 0.5924 (mmtm) outliers start: 38 outliers final: 32 residues processed: 248 average time/residue: 0.3122 time to fit residues: 116.8455 Evaluate side-chains 250 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 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 U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 26 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 2.9990 chunk 133 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN T 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19974 Z= 0.265 Angle : 0.562 9.074 27093 Z= 0.294 Chirality : 0.044 0.205 3279 Planarity : 0.004 0.044 3339 Dihedral : 5.905 59.915 4335 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.47 % Favored : 95.40 % Rotamer: Outliers : 1.81 % Allowed : 11.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2304 helix: 2.04 (0.27), residues: 378 sheet: 0.29 (0.19), residues: 741 loop : -0.54 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 35 HIS 0.003 0.001 HIS I 105 PHE 0.029 0.002 PHE K 67 TYR 0.015 0.001 TYR K 90 ARG 0.007 0.000 ARG S 151 ********************** 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 252 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 2.111 Fit side-chains revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7475 (ttm110) REVERT: A 502 LYS cc_start: 0.6978 (mmtp) cc_final: 0.6526 (mmtt) REVERT: I 136 ASN cc_start: 0.7931 (t0) cc_final: 0.7677 (t0) REVERT: I 217 TYR cc_start: 0.8449 (m-80) cc_final: 0.7953 (m-80) REVERT: I 502 LYS cc_start: 0.7215 (mmtt) cc_final: 0.6153 (mmtm) REVERT: S 502 LYS cc_start: 0.7151 (mmtp) cc_final: 0.6210 (mmtt) outliers start: 37 outliers final: 36 residues processed: 238 average time/residue: 0.3280 time to fit residues: 117.7295 Evaluate side-chains 249 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 35 TRP Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 26 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN I 67 ASN K 52 ASN U 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.090378 restraints weight = 28687.868| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.57 r_work: 0.2783 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19974 Z= 0.214 Angle : 0.537 8.723 27093 Z= 0.283 Chirality : 0.044 0.200 3279 Planarity : 0.004 0.044 3339 Dihedral : 5.779 58.721 4335 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.49 % Rotamer: Outliers : 1.76 % Allowed : 11.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2304 helix: 2.13 (0.27), residues: 378 sheet: 0.34 (0.19), residues: 741 loop : -0.50 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 35 HIS 0.003 0.001 HIS I 105 PHE 0.023 0.001 PHE K 67 TYR 0.014 0.001 TYR U 100G ARG 0.007 0.000 ARG S 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4155.64 seconds wall clock time: 76 minutes 27.81 seconds (4587.81 seconds total)