Starting phenix.real_space_refine on Sat Sep 28 16:20:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/09_2024/6x9r_22108.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/09_2024/6x9r_22108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/09_2024/6x9r_22108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/09_2024/6x9r_22108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/09_2024/6x9r_22108.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/09_2024/6x9r_22108.cif" } resolution = 3.1 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: 12.57, per 1000 atoms: 0.64 Number of scatterers: 19590 At special positions: 0 Unit cell: (122.57, 126.69, 149.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 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=2.06 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=2.17 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=2.15 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=2.04 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=2.06 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=2.17 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=2.15 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=2.04 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=2.06 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=2.16 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=2.15 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=2.04 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: 48 helices and 48 sheets defined 20.6% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.134A 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: 4.048A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.211A 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: 3.756A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.519A 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 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: 4.135A 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: 4.048A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.211A 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: 3.755A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.520A 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 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: 4.134A 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: 4.048A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.210A 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: 3.756A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.519A 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 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: 3.868A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 75 through 76 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: 6.450A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.529A 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: 6.424A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.168A 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: 6.552A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (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: 6.234A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.653A 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: 6.060A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.595A 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 Processing sheet with id=14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.498A 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: 6.566A 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: 3.868A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'I' and resid 75 through 76 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: 6.451A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.529A 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: 6.423A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.563A 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: 10.274A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 4.168A 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: 6.552A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (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: 6.234A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.653A 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: 6.059A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.595A 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 Processing sheet with id=30, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.498A 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: 6.566A 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: 3.869A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL S 242 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'S' and resid 75 through 76 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: 6.450A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.529A 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: 6.424A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL S 442 " --> pdb=" O CYS S 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS S 296 " --> pdb=" O VAL S 442 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N ARG S 444 " --> pdb=" O ILE S 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE S 294 " --> pdb=" O ARG S 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL S 446 " --> pdb=" O VAL S 292 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL S 292 " --> pdb=" O VAL S 446 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN S 448 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR S 290 " --> pdb=" O ASN S 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR S 450 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.414A 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: 6.552A pdb=" N LEU S 260 " --> pdb=" O THR S 450 " (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: 6.233A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.653A 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: 6.060A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.595A 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 Processing sheet with id=46, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.497A 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: 6.566A 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 24 756 hydrogen bonds defined for protein. 1935 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: 7.40 Time building geometry restraints manager: 6.76 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: 3667 1.31 - 1.44: 5373 1.44 - 1.57: 10723 1.57 - 1.69: 40 1.69 - 1.82: 171 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C1 NAG I 603 " pdb=" O5 NAG I 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C1 NAG S 603 " pdb=" O5 NAG S 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 24188 2.67 - 5.33: 2592 5.33 - 8.00: 283 8.00 - 10.67: 24 10.67 - 13.33: 6 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 124.03 -13.33 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 124.02 -13.32 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 123.99 -13.29 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N GLY M 100 " pdb=" CA GLY M 100 " pdb=" C GLY M 100 " ideal model delta sigma weight residual 112.85 100.34 12.51 1.61e+00 3.86e-01 6.04e+01 angle pdb=" C ASP M 50 " pdb=" N VAL M 51 " pdb=" CA VAL M 51 " ideal model delta sigma weight residual 123.16 114.93 8.23 1.06e+00 8.90e-01 6.03e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 12574 21.78 - 43.55: 329 43.55 - 65.33: 93 65.33 - 87.11: 27 87.11 - 108.88: 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 93.00 161.97 -68.97 1 1.00e+01 1.00e-02 6.16e+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 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+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 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 ... (remaining 13035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2322 0.098 - 0.196: 769 0.196 - 0.294: 164 0.294 - 0.392: 18 0.392 - 0.491: 6 Chirality restraints: 3279 Sorted by residual: 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 1.50e+02 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 -2.64 0.24 2.00e-02 2.50e+03 1.49e+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 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.222 2.00e-02 2.50e+03 1.84e-01 4.21e+02 pdb=" C7 NAG T 702 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.222 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" C7 NAG B 702 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.221 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" C7 NAG J 702 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.300 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.019 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4131 2.76 - 3.30: 16799 3.30 - 3.83: 32207 3.83 - 4.37: 38497 4.37 - 4.90: 65141 Nonbonded interactions: 156775 Sorted by model distance: nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.229 3.040 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.283 3.120 nonbonded pdb=" N ASN S 355 " pdb=" OD1 ASN S 355 " model vdw 2.283 3.120 ... (remaining 156770 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 46.420 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.130 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.150 19974 Z= 1.615 Angle : 1.719 13.332 27093 Z= 1.125 Chirality : 0.100 0.491 3279 Planarity : 0.011 0.184 3339 Dihedral : 11.452 108.883 8598 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.30 % Favored : 96.35 % Rotamer: Outliers : 0.44 % Allowed : 0.15 % Favored : 99.41 % 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: 0.53 (0.17), residues: 2304 helix: -0.32 (0.24), residues: 393 sheet: 0.83 (0.20), residues: 630 loop : 0.48 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.012 TRP A 427 HIS 0.008 0.002 HIS U 82A PHE 0.035 0.006 PHE S 383 TYR 0.047 0.007 TYR V 36 ARG 0.008 0.001 ARG U 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 504 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 495 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8521 (mmtp) REVERT: A 150 MET cc_start: 0.8053 (mmm) cc_final: 0.7749 (mmm) REVERT: A 318 TYR cc_start: 0.8763 (m-80) cc_final: 0.8518 (m-80) REVERT: A 492 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8421 (mt-10) REVERT: A 502 LYS cc_start: 0.6886 (mmtp) cc_final: 0.5918 (mmtm) REVERT: L 94 ARG cc_start: 0.5936 (mmt180) cc_final: 0.4510 (mmt180) REVERT: I 150 MET cc_start: 0.7869 (mmm) cc_final: 0.7138 (mmt) REVERT: I 502 LYS cc_start: 0.6375 (mmtp) cc_final: 0.5553 (mmtm) REVERT: J 624 ASP cc_start: 0.8293 (m-30) cc_final: 0.8037 (m-30) REVERT: M 94 ARG cc_start: 0.6376 (mmt180) cc_final: 0.4686 (mtp180) REVERT: S 46 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8562 (mmtp) REVERT: S 502 LYS cc_start: 0.6176 (mmtp) cc_final: 0.5680 (mmtp) REVERT: V 47 MET cc_start: 0.8171 (mmm) cc_final: 0.7801 (mmt) REVERT: V 94 ARG cc_start: 0.6002 (mmt180) cc_final: 0.5111 (mmt180) outliers start: 9 outliers final: 7 residues processed: 500 average time/residue: 0.3612 time to fit residues: 259.9569 Evaluate side-chains 278 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 271 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN J 607 ASN S 103 GLN T 607 ASN U 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19974 Z= 0.224 Angle : 0.686 8.144 27093 Z= 0.366 Chirality : 0.047 0.229 3279 Planarity : 0.004 0.036 3339 Dihedral : 8.696 64.520 4349 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.52 % Favored : 96.22 % Rotamer: Outliers : 1.96 % Allowed : 5.87 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2304 helix: 1.60 (0.28), residues: 384 sheet: 0.41 (0.20), residues: 660 loop : 0.07 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 479 HIS 0.004 0.001 HIS H 82A PHE 0.018 0.002 PHE I 383 TYR 0.015 0.001 TYR L 96 ARG 0.008 0.001 ARG B 542 *********************** 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 384 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 344 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9359 (ptm) cc_final: 0.9059 (ptm) REVERT: A 117 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7735 (mttp) REVERT: A 150 MET cc_start: 0.7933 (mmm) cc_final: 0.7611 (mmm) REVERT: A 371 VAL cc_start: 0.9058 (t) cc_final: 0.8794 (m) REVERT: A 502 LYS cc_start: 0.6796 (mmtp) cc_final: 0.5595 (mmtm) REVERT: I 121 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8445 (mmtp) REVERT: I 426 MET cc_start: 0.8861 (mmt) cc_final: 0.8596 (tpt) REVERT: I 502 LYS cc_start: 0.6429 (mmtp) cc_final: 0.5365 (mmtm) REVERT: J 624 ASP cc_start: 0.8041 (m-30) cc_final: 0.7647 (m-30) REVERT: M 94 ARG cc_start: 0.6044 (mmt180) cc_final: 0.4534 (mmt180) REVERT: S 502 LYS cc_start: 0.6306 (mmtp) cc_final: 0.5739 (mmtp) REVERT: T 607 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8417 (t0) REVERT: V 47 MET cc_start: 0.8170 (mmm) cc_final: 0.7786 (mmt) REVERT: V 94 ARG cc_start: 0.5649 (mmt180) cc_final: 0.4514 (mtp180) outliers start: 40 outliers final: 28 residues processed: 369 average time/residue: 0.3505 time to fit residues: 188.7136 Evaluate side-chains 306 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 277 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 607 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP 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 T residue 607 ASN Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 174 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN I 67 ASN I 377 ASN J 651 ASN S 377 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19974 Z= 0.272 Angle : 0.635 11.527 27093 Z= 0.335 Chirality : 0.047 0.382 3279 Planarity : 0.004 0.051 3339 Dihedral : 7.817 59.120 4347 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 2.20 % Allowed : 7.53 % Favored : 90.27 % 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: 0.48 (0.18), residues: 2304 helix: 1.57 (0.28), residues: 405 sheet: 0.59 (0.20), residues: 651 loop : -0.18 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 96 HIS 0.005 0.001 HIS S 105 PHE 0.016 0.002 PHE S 383 TYR 0.012 0.001 TYR L 96 ARG 0.007 0.001 ARG T 542 *********************** 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 330 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 285 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7712 (mttp) REVERT: A 150 MET cc_start: 0.8047 (mmm) cc_final: 0.7700 (mmm) REVERT: A 502 LYS cc_start: 0.6895 (mmtp) cc_final: 0.5753 (mmtm) REVERT: H 25 SER cc_start: 0.8568 (p) cc_final: 0.8241 (m) REVERT: I 502 LYS cc_start: 0.6597 (mmtp) cc_final: 0.5308 (mmtp) REVERT: J 624 ASP cc_start: 0.8196 (m-30) cc_final: 0.7868 (m-30) REVERT: M 94 ARG cc_start: 0.5877 (mmt180) cc_final: 0.4653 (mmt180) REVERT: S 46 LYS cc_start: 0.8637 (mmtp) cc_final: 0.8367 (mmtp) REVERT: S 67 ASN cc_start: 0.8142 (m-40) cc_final: 0.7923 (m-40) REVERT: S 395 TRP cc_start: 0.6736 (m-10) cc_final: 0.6399 (m-10) REVERT: S 502 LYS cc_start: 0.6661 (mmtp) cc_final: 0.5869 (mmtp) REVERT: U 25 SER cc_start: 0.8658 (p) cc_final: 0.8335 (m) REVERT: V 47 MET cc_start: 0.8159 (mmm) cc_final: 0.7719 (mmt) REVERT: V 94 ARG cc_start: 0.5812 (mmt180) cc_final: 0.4470 (mtp180) outliers start: 45 outliers final: 32 residues processed: 307 average time/residue: 0.3496 time to fit residues: 156.8766 Evaluate side-chains 297 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 265 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain S residue 95 MET Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain V residue 11 VAL 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: 2.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 chunk 223 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN J 651 ASN ** S 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19974 Z= 0.208 Angle : 0.568 9.938 27093 Z= 0.299 Chirality : 0.045 0.361 3279 Planarity : 0.004 0.055 3339 Dihedral : 6.529 55.671 4347 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.53 % Rotamer: Outliers : 2.25 % Allowed : 8.50 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.50 (0.18), residues: 2304 helix: 1.77 (0.28), residues: 402 sheet: 0.54 (0.19), residues: 729 loop : -0.26 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.004 0.001 HIS S 105 PHE 0.015 0.002 PHE I 383 TYR 0.010 0.001 TYR M 49 ARG 0.004 0.000 ARG T 542 *********************** 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 330 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 284 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7730 (mttp) REVERT: A 150 MET cc_start: 0.8044 (mmm) cc_final: 0.7689 (mmm) REVERT: A 371 VAL cc_start: 0.9078 (t) cc_final: 0.8786 (m) REVERT: A 502 LYS cc_start: 0.6914 (mmtp) cc_final: 0.5738 (mmtm) REVERT: H 25 SER cc_start: 0.8601 (p) cc_final: 0.8322 (m) REVERT: I 502 LYS cc_start: 0.6631 (mmtp) cc_final: 0.5302 (mmtp) REVERT: J 624 ASP cc_start: 0.8357 (m-30) cc_final: 0.7945 (m-30) REVERT: S 395 TRP cc_start: 0.6736 (m-10) cc_final: 0.6525 (m-10) REVERT: S 502 LYS cc_start: 0.6710 (mmtp) cc_final: 0.5781 (mmtp) REVERT: U 25 SER cc_start: 0.8708 (p) cc_final: 0.8443 (m) REVERT: V 47 MET cc_start: 0.8218 (mmm) cc_final: 0.7851 (mmt) REVERT: V 94 ARG cc_start: 0.5789 (mmt180) cc_final: 0.4450 (mtp180) outliers start: 46 outliers final: 29 residues processed: 307 average time/residue: 0.3536 time to fit residues: 159.1973 Evaluate side-chains 293 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 264 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 6.9990 chunk 126 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 651 ASN S 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19974 Z= 0.235 Angle : 0.577 8.651 27093 Z= 0.301 Chirality : 0.046 0.364 3279 Planarity : 0.004 0.055 3339 Dihedral : 6.790 108.782 4347 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 2.49 % Allowed : 8.99 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.45 (0.18), residues: 2304 helix: 1.81 (0.27), residues: 402 sheet: 0.49 (0.19), residues: 729 loop : -0.31 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 427 HIS 0.005 0.001 HIS A 105 PHE 0.015 0.002 PHE S 383 TYR 0.020 0.001 TYR M 49 ARG 0.003 0.000 ARG S 480 *********************** 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 325 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 274 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7735 (mttp) REVERT: A 150 MET cc_start: 0.8065 (mmm) cc_final: 0.7705 (mmm) REVERT: A 371 VAL cc_start: 0.9125 (t) cc_final: 0.8818 (m) REVERT: A 502 LYS cc_start: 0.6899 (mmtp) cc_final: 0.5649 (mmtm) REVERT: H 25 SER cc_start: 0.8655 (p) cc_final: 0.8377 (m) REVERT: I 502 LYS cc_start: 0.6670 (mmtp) cc_final: 0.5279 (mmtp) REVERT: J 624 ASP cc_start: 0.8248 (m-30) cc_final: 0.7905 (m-30) REVERT: M 79 GLN cc_start: 0.7987 (mp10) cc_final: 0.7413 (mp10) REVERT: S 395 TRP cc_start: 0.6798 (m-10) cc_final: 0.6325 (m-10) REVERT: S 502 LYS cc_start: 0.6797 (mmtp) cc_final: 0.5849 (mmtp) REVERT: T 626 MET cc_start: 0.8882 (mtt) cc_final: 0.8429 (ttm) REVERT: U 25 SER cc_start: 0.8783 (p) cc_final: 0.8534 (m) REVERT: V 47 MET cc_start: 0.8137 (mmm) cc_final: 0.7799 (mmt) REVERT: V 94 ARG cc_start: 0.5819 (mmt180) cc_final: 0.4458 (mmt180) outliers start: 51 outliers final: 34 residues processed: 297 average time/residue: 0.3579 time to fit residues: 155.6465 Evaluate side-chains 298 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 264 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 95 MET Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 111 VAL Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN L 79 GLN J 607 ASN J 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 19974 Z= 0.361 Angle : 0.630 9.006 27093 Z= 0.327 Chirality : 0.048 0.535 3279 Planarity : 0.004 0.058 3339 Dihedral : 6.748 106.818 4347 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.21 % Favored : 94.66 % Rotamer: Outliers : 2.49 % Allowed : 9.29 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.27 (0.18), residues: 2304 helix: 1.58 (0.27), residues: 405 sheet: 0.40 (0.19), residues: 729 loop : -0.41 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 571 HIS 0.006 0.001 HIS A 105 PHE 0.023 0.002 PHE S 383 TYR 0.026 0.002 TYR M 49 ARG 0.005 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 320 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 269 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7758 (mmmt) REVERT: A 150 MET cc_start: 0.8100 (mmm) cc_final: 0.7723 (mmm) REVERT: A 371 VAL cc_start: 0.9132 (t) cc_final: 0.8818 (m) REVERT: A 502 LYS cc_start: 0.6960 (mmtp) cc_final: 0.5669 (mmtm) REVERT: H 25 SER cc_start: 0.8793 (p) cc_final: 0.8543 (m) REVERT: H 100 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9230 (mt) REVERT: I 502 LYS cc_start: 0.6790 (mmtp) cc_final: 0.5476 (mmtm) REVERT: J 624 ASP cc_start: 0.8171 (m-30) cc_final: 0.7911 (m-30) REVERT: K 100 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9051 (mp) REVERT: M 79 GLN cc_start: 0.8015 (mp10) cc_final: 0.7382 (mp10) REVERT: S 395 TRP cc_start: 0.6877 (m-10) cc_final: 0.6427 (m-10) REVERT: S 502 LYS cc_start: 0.6925 (mmtp) cc_final: 0.6016 (mmtp) REVERT: U 25 SER cc_start: 0.8859 (p) cc_final: 0.8648 (m) REVERT: V 47 MET cc_start: 0.8098 (mmm) cc_final: 0.7770 (mmt) REVERT: V 94 ARG cc_start: 0.5965 (mmt180) cc_final: 0.4649 (mmt180) outliers start: 51 outliers final: 40 residues processed: 301 average time/residue: 0.3529 time to fit residues: 155.5577 Evaluate side-chains 302 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 260 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 95 MET Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 0.0070 chunk 163 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 188 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 651 ASN M 17 GLN S 377 ASN V 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19974 Z= 0.171 Angle : 0.561 11.880 27093 Z= 0.292 Chirality : 0.048 0.865 3279 Planarity : 0.004 0.056 3339 Dihedral : 6.525 114.215 4347 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 2.25 % Allowed : 9.87 % Favored : 87.88 % 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: 0.45 (0.18), residues: 2304 helix: 2.00 (0.27), residues: 402 sheet: 0.48 (0.19), residues: 732 loop : -0.38 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 623 HIS 0.003 0.001 HIS S 105 PHE 0.014 0.001 PHE A 53 TYR 0.021 0.001 TYR M 49 ARG 0.003 0.000 ARG I 166 *********************** 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 320 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 274 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7788 (mmmt) REVERT: A 150 MET cc_start: 0.8049 (mmm) cc_final: 0.7693 (mmm) REVERT: A 371 VAL cc_start: 0.9070 (t) cc_final: 0.8774 (m) REVERT: A 502 LYS cc_start: 0.6906 (mmtp) cc_final: 0.5614 (mmtm) REVERT: H 43 LYS cc_start: 0.8671 (mmtm) cc_final: 0.8435 (mmmm) REVERT: I 502 LYS cc_start: 0.6613 (mmtp) cc_final: 0.5242 (mmtp) REVERT: M 79 GLN cc_start: 0.8017 (mp10) cc_final: 0.7780 (mp10) REVERT: S 395 TRP cc_start: 0.6838 (m-10) cc_final: 0.6461 (m-10) REVERT: S 502 LYS cc_start: 0.6837 (mmtp) cc_final: 0.6041 (mmtp) REVERT: T 626 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8730 (mmt) REVERT: U 25 SER cc_start: 0.8848 (p) cc_final: 0.8641 (m) REVERT: V 47 MET cc_start: 0.8069 (mmm) cc_final: 0.7730 (mmt) outliers start: 46 outliers final: 34 residues processed: 296 average time/residue: 0.3525 time to fit residues: 152.7128 Evaluate side-chains 299 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19974 Z= 0.314 Angle : 0.598 7.591 27093 Z= 0.311 Chirality : 0.047 0.506 3279 Planarity : 0.004 0.058 3339 Dihedral : 6.595 112.494 4347 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.16 % Favored : 94.70 % Rotamer: Outliers : 2.20 % Allowed : 10.31 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.77 (0.27), residues: 405 sheet: 0.26 (0.18), residues: 750 loop : -0.47 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.005 0.001 HIS S 105 PHE 0.018 0.002 PHE S 383 TYR 0.021 0.001 TYR M 49 ARG 0.004 0.000 ARG S 480 *********************** 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 309 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 264 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7795 (mmmt) REVERT: A 150 MET cc_start: 0.8099 (mmm) cc_final: 0.7735 (mmm) REVERT: A 371 VAL cc_start: 0.9104 (t) cc_final: 0.8802 (m) REVERT: A 502 LYS cc_start: 0.6930 (mmtp) cc_final: 0.5590 (mmtp) REVERT: H 25 SER cc_start: 0.8861 (p) cc_final: 0.8652 (m) REVERT: I 502 LYS cc_start: 0.6806 (mmtp) cc_final: 0.5478 (mmtm) REVERT: M 79 GLN cc_start: 0.8056 (mp10) cc_final: 0.7395 (mp10) REVERT: S 395 TRP cc_start: 0.6959 (m-10) cc_final: 0.6570 (m-10) REVERT: S 502 LYS cc_start: 0.6873 (mmtp) cc_final: 0.5633 (mmtm) REVERT: V 47 MET cc_start: 0.8020 (mmm) cc_final: 0.7687 (mmt) outliers start: 45 outliers final: 37 residues processed: 291 average time/residue: 0.3496 time to fit residues: 148.7796 Evaluate side-chains 291 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 246 GLN V 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19974 Z= 0.165 Angle : 0.548 10.659 27093 Z= 0.286 Chirality : 0.045 0.343 3279 Planarity : 0.004 0.056 3339 Dihedral : 6.413 114.709 4347 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.82 % Favored : 95.10 % Rotamer: Outliers : 2.00 % Allowed : 10.75 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.18), residues: 2304 helix: 2.12 (0.27), residues: 402 sheet: 0.46 (0.19), residues: 726 loop : -0.43 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.004 0.001 HIS A 105 PHE 0.014 0.001 PHE A 53 TYR 0.019 0.001 TYR M 49 ARG 0.004 0.000 ARG B 585 *********************** 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 304 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7795 (mmmt) REVERT: A 150 MET cc_start: 0.8070 (mmm) cc_final: 0.7732 (mmm) REVERT: A 371 VAL cc_start: 0.9065 (t) cc_final: 0.8803 (m) REVERT: A 502 LYS cc_start: 0.6883 (mmtp) cc_final: 0.5420 (mmtm) REVERT: I 502 LYS cc_start: 0.6689 (mmtp) cc_final: 0.5303 (mmtp) REVERT: M 27 ASP cc_start: 0.7419 (t0) cc_final: 0.7123 (t0) REVERT: M 79 GLN cc_start: 0.8034 (mp10) cc_final: 0.7439 (mp10) REVERT: S 395 TRP cc_start: 0.6836 (m-10) cc_final: 0.6490 (m-10) REVERT: S 502 LYS cc_start: 0.6788 (mmtp) cc_final: 0.5676 (mmtm) REVERT: T 626 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8774 (mmt) REVERT: V 47 MET cc_start: 0.8015 (mmm) cc_final: 0.7658 (mmt) outliers start: 41 outliers final: 33 residues processed: 286 average time/residue: 0.3347 time to fit residues: 141.9334 Evaluate side-chains 291 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 257 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL 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: 0.0470 chunk 104 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 230 optimal weight: 0.0270 chunk 211 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 overall best weight: 1.3740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19974 Z= 0.204 Angle : 0.549 10.486 27093 Z= 0.287 Chirality : 0.046 0.578 3279 Planarity : 0.004 0.057 3339 Dihedral : 7.051 114.391 4345 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.30 % Favored : 94.66 % Rotamer: Outliers : 1.86 % Allowed : 11.00 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2304 helix: 2.17 (0.27), residues: 402 sheet: 0.47 (0.19), residues: 726 loop : -0.43 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 427 HIS 0.004 0.001 HIS A 105 PHE 0.014 0.001 PHE A 53 TYR 0.020 0.001 TYR M 49 ARG 0.003 0.000 ARG B 585 ********************** 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 297 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 259 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7813 (mmmt) REVERT: A 502 LYS cc_start: 0.6869 (mmtp) cc_final: 0.5421 (mmtm) REVERT: I 502 LYS cc_start: 0.6747 (mmtp) cc_final: 0.5252 (mmtp) REVERT: M 27 ASP cc_start: 0.7429 (t0) cc_final: 0.7171 (t0) REVERT: M 61 ARG cc_start: 0.7858 (mtm110) cc_final: 0.7613 (mtm110) REVERT: M 79 GLN cc_start: 0.8001 (mp10) cc_final: 0.7379 (mp10) REVERT: S 395 TRP cc_start: 0.6848 (m-10) cc_final: 0.6504 (m-10) REVERT: S 502 LYS cc_start: 0.6841 (mmtp) cc_final: 0.6049 (mmtp) REVERT: T 626 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8734 (mmt) REVERT: V 47 MET cc_start: 0.8026 (mmm) cc_final: 0.7658 (mmt) outliers start: 38 outliers final: 35 residues processed: 281 average time/residue: 0.3594 time to fit residues: 149.1111 Evaluate side-chains 292 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 256 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL 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: 0.9980 chunk 168 optimal weight: 0.1980 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 188 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 246 GLN V 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.093539 restraints weight = 27247.291| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.53 r_work: 0.2845 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19974 Z= 0.140 Angle : 0.511 10.357 27093 Z= 0.267 Chirality : 0.044 0.359 3279 Planarity : 0.004 0.055 3339 Dihedral : 6.686 112.224 4343 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.30 % Favored : 95.66 % Rotamer: Outliers : 1.76 % Allowed : 11.09 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2304 helix: 2.71 (0.27), residues: 384 sheet: 0.56 (0.19), residues: 714 loop : -0.45 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 427 HIS 0.003 0.001 HIS A 105 PHE 0.014 0.001 PHE A 53 TYR 0.020 0.001 TYR M 49 ARG 0.006 0.000 ARG A 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4400.57 seconds wall clock time: 79 minutes 8.56 seconds (4748.56 seconds total)