Starting phenix.real_space_refine on Sun May 18 21:38:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evz_50020/05_2025/9evz_50020.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evz_50020/05_2025/9evz_50020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9evz_50020/05_2025/9evz_50020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evz_50020/05_2025/9evz_50020.map" model { file = "/net/cci-nas-00/data/ceres_data/9evz_50020/05_2025/9evz_50020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evz_50020/05_2025/9evz_50020.cif" } resolution = 2.92 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= 0.001 sd= 0.021 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 115 5.16 5 C 10947 2.51 5 N 2950 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17512 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3473 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 905 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "G" Number of atoms: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3443 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3470 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1711 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 217} Chain: "L" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1629 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" 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: "k" 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 10.89, per 1000 atoms: 0.62 Number of scatterers: 17512 At special positions: 0 Unit cell: (131.1, 120.65, 187.15, 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 115 16.00 O 3500 8.00 N 2950 7.00 C 10947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 216 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 ALPHA1-2 " MAN e 4 " - " MAN e 5 " ALPHA1-3 " BMA e 3 " - " MAN e 4 " " BMA j 3 " - " MAN j 4 " " BMA k 3 " - " MAN k 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG u 1 " - " NAG u 2 " NAG-ASN " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 295 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 363 " " NAG C 608 " - " ASN C 339 " " NAG C 609 " - " ASN C 160 " " NAG D 1 " - " ASN I 386 " " NAG E 1 " - " ASN I 363 " " NAG F 701 " - " ASN F 637 " " NAG G 601 " - " ASN G 160 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 301 " " NAG G 604 " - " ASN G 448 " " NAG G 605 " - " ASN G 295 " " NAG G 606 " - " ASN G 392 " " NAG G 607 " - " ASN G 363 " " NAG G 608 " - " ASN G 276 " " NAG G 609 " - " ASN G 197 " " NAG G 610 " - " ASN G 234 " " NAG I 601 " - " ASN I 234 " " NAG I 602 " - " ASN I 392 " " NAG I 603 " - " ASN I 301 " " NAG I 604 " - " ASN I 355 " " NAG I 605 " - " ASN I 339 " " NAG I 606 " - " ASN I 197 " " NAG I 607 " - " ASN I 160 " " NAG J 1 " - " ASN I 332 " " NAG K 1 " - " ASN I 156 " " NAG M 1 " - " ASN I 448 " " NAG N 1 " - " ASN I 295 " " NAG P 1 " - " ASN C 448 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 156 " " NAG U 1 " - " ASN G 156 " " NAG V 1 " - " ASN G 332 " " NAG W 1 " - " ASN G 386 " " NAG e 1 " - " ASN I 262 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN G 262 " " NAG q 1 " - " ASN I 88 " " NAG u 1 " - " ASN I 276 " Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 2.2 seconds 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3926 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 38 sheets defined 20.1% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.912A pdb=" N MET A 535 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.762A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 595 removed outlier: 3.511A pdb=" N ARG A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.833A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.529A pdb=" N SER B 534 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 531 through 535' Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.052A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.846A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.687A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 656 removed outlier: 3.522A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.009A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.101A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.536A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.679A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.532A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.544A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.572A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.742A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 115 removed outlier: 4.092A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.631A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.767A pdb=" N ARG G 151 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 4.327A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.540A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.667A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.399A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN I 103 " --> pdb=" O ASN I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 126 Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.589A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.652A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 129 No H-bonds generated for 'chain 'H' and resid 127 through 129' Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.735A pdb=" N SER L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 5.150A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 4.584A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.321A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.545A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.504A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 177 removed outlier: 4.261A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.469A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.383A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 298 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.213A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.061A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.213A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 298 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.444A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 603 through 609 removed outlier: 5.528A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.793A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 177 removed outlier: 4.350A pdb=" N GLU G 190 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.248A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.304A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG G 298 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.172A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 12.185A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.167A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.167A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.185A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 12.172A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG G 298 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.341A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.469A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AC3, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.597A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 120 through 121 removed outlier: 3.829A pdb=" N VAL I 120 " --> pdb=" O GLN I 203 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 169 through 177 removed outlier: 3.546A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU I 190 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.246A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.098A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.933A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.926A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 271 through 273 removed outlier: 10.926A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.933A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 12.098A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.626A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.622A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'H' and resid 97 through 99 Processing sheet with id=AD4, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.981A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 131 through 132 removed outlier: 5.981A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.351A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.496A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU L 33 " --> pdb=" O THR L 49 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.496A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.770A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 153 through 154 663 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5484 1.34 - 1.47: 4510 1.47 - 1.59: 7710 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 17858 Sorted by residual: bond pdb=" CB LYS L 190 " pdb=" CG LYS L 190 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CB GLN G 246 " pdb=" CG GLN G 246 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CB GLN I 82 " pdb=" CG GLN I 82 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB LYS L 145 " pdb=" CG LYS L 145 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.42e+00 bond pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " ideal model delta sigma weight residual 1.808 1.844 -0.036 3.30e-02 9.18e+02 1.18e+00 ... (remaining 17853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 23895 2.02 - 4.04: 303 4.04 - 6.06: 34 6.06 - 8.07: 9 8.07 - 10.09: 6 Bond angle restraints: 24247 Sorted by residual: angle pdb=" CA GLN G 246 " pdb=" CB GLN G 246 " pdb=" CG GLN G 246 " ideal model delta sigma weight residual 114.10 122.20 -8.10 2.00e+00 2.50e-01 1.64e+01 angle pdb=" CB LYS L 190 " pdb=" CG LYS L 190 " pdb=" CD LYS L 190 " ideal model delta sigma weight residual 111.30 119.66 -8.36 2.30e+00 1.89e-01 1.32e+01 angle pdb=" C HIS H 200 " pdb=" N LYS H 201 " pdb=" CA LYS H 201 " ideal model delta sigma weight residual 120.09 124.42 -4.33 1.25e+00 6.40e-01 1.20e+01 angle pdb=" C2 NAG C 609 " pdb=" N2 NAG C 609 " pdb=" C7 NAG C 609 " ideal model delta sigma weight residual 124.56 134.37 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C2 NAG I 607 " pdb=" N2 NAG I 607 " pdb=" C7 NAG I 607 " ideal model delta sigma weight residual 124.56 134.37 -9.81 3.00e+00 1.11e-01 1.07e+01 ... (remaining 24242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 10489 17.82 - 35.64: 876 35.64 - 53.45: 249 53.45 - 71.27: 56 71.27 - 89.09: 26 Dihedral angle restraints: 11696 sinusoidal: 5617 harmonic: 6079 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -175.00 89.00 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual -86.00 -3.76 -82.24 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 445 " pdb=" CB CYS I 445 " ideal model delta sinusoidal sigma weight residual -86.00 -144.06 58.06 1 1.00e+01 1.00e-02 4.52e+01 ... (remaining 11693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2710 0.086 - 0.172: 234 0.172 - 0.257: 4 0.257 - 0.343: 2 0.343 - 0.429: 1 Chirality restraints: 2951 Sorted by residual: chirality pdb=" C1 NAG C 603 " pdb=" ND2 ASN C 355 " pdb=" C2 NAG C 603 " pdb=" O5 NAG C 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" C2 NAG C 609 " pdb=" C1 NAG C 609 " pdb=" C3 NAG C 609 " pdb=" N2 NAG C 609 " both_signs ideal model delta sigma weight residual False -2.49 -2.21 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C2 NAG I 607 " pdb=" C1 NAG I 607 " pdb=" C3 NAG I 607 " pdb=" N2 NAG I 607 " both_signs ideal model delta sigma weight residual False -2.49 -2.23 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2948 not shown) Planarity restraints: 3042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 355 " 0.029 2.00e-02 2.50e+03 2.79e-02 9.71e+00 pdb=" CG ASN C 355 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN C 355 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 355 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG C 603 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.020 2.00e-02 2.50e+03 1.84e-02 4.24e+00 pdb=" CG ASN C 234 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.016 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 246 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C GLN G 246 " -0.034 2.00e-02 2.50e+03 pdb=" O GLN G 246 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS G 247 " 0.011 2.00e-02 2.50e+03 ... (remaining 3039 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1047 2.74 - 3.28: 15363 3.28 - 3.82: 27039 3.82 - 4.36: 33190 4.36 - 4.90: 58482 Nonbonded interactions: 135121 Sorted by model distance: nonbonded pdb=" O LEU G 369 " pdb=" OG1 THR G 373 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP A 632 " pdb=" NZ LYS C 46 " model vdw 2.222 3.120 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.223 3.040 nonbonded pdb=" N GLN C 246 " pdb=" OE1 GLN C 246 " model vdw 2.229 3.120 ... (remaining 135116 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 'A' and (resid 522 through 538 or (resid 568 and (name N or name CA or na \ me C or name O or name CB )) or resid 569 through 656)) selection = (chain 'B' and (resid 522 through 538 or resid 568 through 656)) selection = (chain 'F' and (resid 522 through 538 or (resid 568 and (name N or name CA or na \ me C or name O or name CB )) or resid 569 through 654 or (resid 655 and (name N \ or name CA or name C or name O or name CB )) or resid 656)) } ncs_group { reference = (chain 'C' and (resid 34 through 56 or resid 66 through 504 or resid 601 through \ 607)) selection = (chain 'G' and (resid 34 through 504 or resid 601 through 607)) selection = (chain 'I' and (resid 34 through 56 or resid 66 through 504 or resid 601 through \ 607)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'u' } ncs_group { reference = chain 'j' selection = chain 'k' } 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=0.00 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: 7.450 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 42.380 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 : 0.003 0.041 17964 Z= 0.140 Angle : 0.649 10.093 24533 Z= 0.340 Chirality : 0.045 0.429 2951 Planarity : 0.004 0.047 2996 Dihedral : 14.376 89.091 7674 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.52 % Allowed : 15.33 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 0.10 (0.18), residues: 2073 helix: 0.55 (0.29), residues: 387 sheet: 1.20 (0.21), residues: 592 loop : -0.76 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 69 HIS 0.004 0.001 HIS G 249 PHE 0.018 0.001 PHE H 51 TYR 0.016 0.001 TYR C 318 ARG 0.006 0.000 ARG C 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 46) link_NAG-ASN : angle 2.30991 ( 138) link_BETA1-4 : bond 0.00573 ( 24) link_BETA1-4 : angle 1.74494 ( 72) link_ALPHA1-2 : bond 0.00590 ( 1) link_ALPHA1-2 : angle 1.29956 ( 3) link_ALPHA1-3 : bond 0.01143 ( 3) link_ALPHA1-3 : angle 1.05906 ( 9) hydrogen bonds : bond 0.14081 ( 623) hydrogen bonds : angle 5.69023 ( 1788) SS BOND : bond 0.00217 ( 32) SS BOND : angle 1.09928 ( 64) covalent geometry : bond 0.00297 (17858) covalent geometry : angle 0.61883 (24247) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 385 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7587 (ttp80) REVERT: F 652 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7819 (mm-40) REVERT: G 40 TYR cc_start: 0.8331 (t80) cc_final: 0.8085 (t80) REVERT: G 211 GLU cc_start: 0.7558 (tp30) cc_final: 0.7347 (tp30) REVERT: G 217 TYR cc_start: 0.7834 (m-80) cc_final: 0.7429 (m-80) REVERT: G 327 ARG cc_start: 0.6939 (mtm110) cc_final: 0.6612 (mtm110) REVERT: G 475 MET cc_start: 0.7821 (tpp) cc_final: 0.7541 (mmm) REVERT: G 484 TYR cc_start: 0.8335 (p90) cc_final: 0.8133 (p90) REVERT: I 164 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6893 (mt-10) REVERT: I 308 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7531 (mtm-85) REVERT: H 21 SER cc_start: 0.7907 (p) cc_final: 0.7700 (t) REVERT: H 86 ASP cc_start: 0.7825 (m-30) cc_final: 0.7371 (m-30) REVERT: H 198 VAL cc_start: 0.6029 (OUTLIER) cc_final: 0.5806 (m) REVERT: L 4 LEU cc_start: 0.8483 (mt) cc_final: 0.8272 (mp) REVERT: L 5 THR cc_start: 0.8436 (m) cc_final: 0.8078 (p) REVERT: L 97 THR cc_start: 0.8077 (p) cc_final: 0.7866 (t) outliers start: 28 outliers final: 8 residues processed: 400 average time/residue: 1.3614 time to fit residues: 604.3477 Evaluate side-chains 363 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 353 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 308 ARG Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 chunk 63 optimal weight: 0.0270 chunk 99 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 188 optimal weight: 0.0270 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN A 653 GLN C 85 HIS C 103 GLN C 440 GLN F 607 ASN F 653 GLN G 289 ASN G 440 GLN I 99 ASN I 188 ASN I 302 ASN I 348 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114723 restraints weight = 25341.595| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.73 r_work: 0.3298 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17964 Z= 0.126 Angle : 0.600 9.647 24533 Z= 0.294 Chirality : 0.045 0.274 2951 Planarity : 0.004 0.050 2996 Dihedral : 6.570 73.312 3817 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.30 % Allowed : 16.58 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 0.31 (0.18), residues: 2073 helix: 0.89 (0.29), residues: 386 sheet: 1.21 (0.20), residues: 619 loop : -0.65 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 112 HIS 0.004 0.001 HIS L 189 PHE 0.020 0.001 PHE H 51 TYR 0.013 0.001 TYR C 173 ARG 0.008 0.001 ARG G 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 46) link_NAG-ASN : angle 2.03592 ( 138) link_BETA1-4 : bond 0.00541 ( 24) link_BETA1-4 : angle 1.65640 ( 72) link_ALPHA1-2 : bond 0.00521 ( 1) link_ALPHA1-2 : angle 1.44616 ( 3) link_ALPHA1-3 : bond 0.01055 ( 3) link_ALPHA1-3 : angle 1.06667 ( 9) hydrogen bonds : bond 0.04595 ( 623) hydrogen bonds : angle 4.79619 ( 1788) SS BOND : bond 0.00288 ( 32) SS BOND : angle 1.31495 ( 64) covalent geometry : bond 0.00287 (17858) covalent geometry : angle 0.57207 (24247) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 368 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: C 130 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7895 (mm-40) REVERT: C 207 LYS cc_start: 0.8296 (pttm) cc_final: 0.7896 (pttm) REVERT: C 217 TYR cc_start: 0.8365 (m-80) cc_final: 0.8146 (m-80) REVERT: C 308 ARG cc_start: 0.8796 (mtm-85) cc_final: 0.8537 (ttp-170) REVERT: C 482 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7965 (tp30) REVERT: C 500 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7862 (mtp85) REVERT: F 535 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7761 (mmm) REVERT: F 607 ASN cc_start: 0.8370 (t0) cc_final: 0.8154 (t0) REVERT: F 652 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7859 (mm-40) REVERT: G 40 TYR cc_start: 0.8608 (t80) cc_final: 0.8336 (t80) REVERT: G 217 TYR cc_start: 0.8180 (m-80) cc_final: 0.7911 (m-80) REVERT: G 256 SER cc_start: 0.9075 (p) cc_final: 0.8847 (t) REVERT: G 327 ARG cc_start: 0.7433 (mtm110) cc_final: 0.7101 (mtm110) REVERT: G 346 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8471 (t) REVERT: G 360 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6483 (ptp-110) REVERT: G 444 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.8075 (ttt90) REVERT: G 467 THR cc_start: 0.7993 (m) cc_final: 0.7733 (p) REVERT: G 484 TYR cc_start: 0.8555 (p90) cc_final: 0.8340 (p90) REVERT: I 113 ASP cc_start: 0.8490 (m-30) cc_final: 0.8273 (m-30) REVERT: I 231 LYS cc_start: 0.8720 (mttt) cc_final: 0.8468 (mttp) REVERT: I 239 CYS cc_start: 0.6944 (t) cc_final: 0.6690 (t) REVERT: I 308 ARG cc_start: 0.8297 (mtp85) cc_final: 0.8042 (mtm-85) REVERT: H 21 SER cc_start: 0.8102 (p) cc_final: 0.7870 (t) REVERT: L 97 THR cc_start: 0.8266 (p) cc_final: 0.8009 (t) REVERT: L 176 SER cc_start: 0.5860 (OUTLIER) cc_final: 0.5227 (m) outliers start: 61 outliers final: 18 residues processed: 399 average time/residue: 1.2737 time to fit residues: 566.7515 Evaluate side-chains 378 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 355 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 117 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN G 103 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 ASN G 348 GLN G 440 GLN I 348 GLN L 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110742 restraints weight = 25317.855| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.92 r_work: 0.3234 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 17964 Z= 0.233 Angle : 0.691 10.885 24533 Z= 0.338 Chirality : 0.048 0.306 2951 Planarity : 0.005 0.049 2996 Dihedral : 6.357 58.082 3804 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.52 % Allowed : 17.55 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2073 helix: 0.65 (0.28), residues: 392 sheet: 1.24 (0.20), residues: 617 loop : -0.79 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 112 HIS 0.008 0.002 HIS C 216 PHE 0.030 0.002 PHE H 51 TYR 0.017 0.002 TYR C 173 ARG 0.007 0.001 ARG I 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 46) link_NAG-ASN : angle 2.33643 ( 138) link_BETA1-4 : bond 0.00510 ( 24) link_BETA1-4 : angle 1.71617 ( 72) link_ALPHA1-2 : bond 0.00582 ( 1) link_ALPHA1-2 : angle 1.36673 ( 3) link_ALPHA1-3 : bond 0.01041 ( 3) link_ALPHA1-3 : angle 1.05274 ( 9) hydrogen bonds : bond 0.06094 ( 623) hydrogen bonds : angle 4.96954 ( 1788) SS BOND : bond 0.00464 ( 32) SS BOND : angle 1.60168 ( 64) covalent geometry : bond 0.00569 (17858) covalent geometry : angle 0.65980 (24247) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 381 time to evaluate : 1.910 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: C 83 GLU cc_start: 0.7970 (tt0) cc_final: 0.7672 (tt0) REVERT: C 123 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8120 (p) REVERT: C 130 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7630 (mm-40) REVERT: C 207 LYS cc_start: 0.8213 (pttm) cc_final: 0.7979 (pttm) REVERT: C 217 TYR cc_start: 0.8231 (m-80) cc_final: 0.8021 (m-80) REVERT: C 482 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8032 (mm-30) REVERT: C 500 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7808 (mtp85) REVERT: F 535 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8045 (mmt) REVERT: F 607 ASN cc_start: 0.8257 (t0) cc_final: 0.8043 (t0) REVERT: F 652 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7676 (mm-40) REVERT: G 153 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6946 (mm-30) REVERT: G 175 LEU cc_start: 0.8317 (mp) cc_final: 0.8080 (mp) REVERT: G 211 GLU cc_start: 0.7724 (tp30) cc_final: 0.7323 (tp30) REVERT: G 256 SER cc_start: 0.8987 (p) cc_final: 0.8708 (t) REVERT: G 327 ARG cc_start: 0.7429 (mtm110) cc_final: 0.7079 (mtm110) REVERT: G 467 THR cc_start: 0.7993 (m) cc_final: 0.7763 (p) REVERT: G 484 TYR cc_start: 0.8535 (p90) cc_final: 0.8201 (p90) REVERT: G 492 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: I 46 LYS cc_start: 0.7840 (mttt) cc_final: 0.7610 (mttt) REVERT: I 178 ARG cc_start: 0.7955 (ttp-170) cc_final: 0.7691 (ttp-170) REVERT: I 239 CYS cc_start: 0.6698 (t) cc_final: 0.6417 (t) REVERT: H 21 SER cc_start: 0.8083 (p) cc_final: 0.7855 (t) REVERT: H 80 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7872 (ttm) REVERT: H 200 HIS cc_start: 0.7116 (t-170) cc_final: 0.6910 (t-170) REVERT: L 89 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8364 (tt0) REVERT: L 97 THR cc_start: 0.8127 (p) cc_final: 0.7845 (t) outliers start: 65 outliers final: 40 residues processed: 410 average time/residue: 1.2918 time to fit residues: 591.3404 Evaluate side-chains 411 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 367 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 492 GLU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 232 LYS Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 66 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 74 optimal weight: 0.0270 chunk 187 optimal weight: 4.9990 chunk 38 optimal weight: 0.0030 chunk 160 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 36 optimal weight: 0.0980 chunk 175 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 overall best weight: 0.1648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN B 590 GLN C 315 GLN C 425 ASN C 440 GLN G 103 GLN G 289 ASN G 293 GLN G 348 GLN G 440 GLN I 85 HIS I 136 ASN I 137 ASN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN L 6 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.145328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114823 restraints weight = 25128.772| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.72 r_work: 0.3295 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17964 Z= 0.098 Angle : 0.568 9.585 24533 Z= 0.275 Chirality : 0.044 0.345 2951 Planarity : 0.004 0.042 2996 Dihedral : 5.990 56.527 3804 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.20 % Allowed : 18.63 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 0.47 (0.19), residues: 2073 helix: 1.28 (0.29), residues: 382 sheet: 1.27 (0.20), residues: 617 loop : -0.64 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 69 HIS 0.004 0.001 HIS H 200 PHE 0.016 0.001 PHE H 51 TYR 0.018 0.001 TYR I 173 ARG 0.009 0.000 ARG I 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 46) link_NAG-ASN : angle 1.94148 ( 138) link_BETA1-4 : bond 0.00551 ( 24) link_BETA1-4 : angle 1.62945 ( 72) link_ALPHA1-2 : bond 0.00573 ( 1) link_ALPHA1-2 : angle 1.40546 ( 3) link_ALPHA1-3 : bond 0.00966 ( 3) link_ALPHA1-3 : angle 1.09680 ( 9) hydrogen bonds : bond 0.04093 ( 623) hydrogen bonds : angle 4.61019 ( 1788) SS BOND : bond 0.00228 ( 32) SS BOND : angle 1.03825 ( 64) covalent geometry : bond 0.00207 (17858) covalent geometry : angle 0.54147 (24247) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 371 time to evaluate : 1.809 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 545 LEU cc_start: 0.8612 (tp) cc_final: 0.8374 (mt) REVERT: C 123 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8181 (p) REVERT: C 207 LYS cc_start: 0.8224 (pttm) cc_final: 0.7992 (pttm) REVERT: C 217 TYR cc_start: 0.8364 (m-80) cc_final: 0.8114 (m-80) REVERT: C 482 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7987 (mm-30) REVERT: C 502 LYS cc_start: 0.8426 (tttt) cc_final: 0.8183 (ttmt) REVERT: F 652 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7894 (mm-40) REVERT: G 175 LEU cc_start: 0.8353 (mp) cc_final: 0.8096 (mp) REVERT: G 327 ARG cc_start: 0.7648 (mtm110) cc_final: 0.7297 (mtm180) REVERT: G 360 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6636 (ptm-80) REVERT: G 484 TYR cc_start: 0.8544 (p90) cc_final: 0.8263 (p90) REVERT: G 492 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: I 46 LYS cc_start: 0.8034 (mttt) cc_final: 0.7778 (mttt) REVERT: I 113 ASP cc_start: 0.8509 (m-30) cc_final: 0.8269 (m-30) REVERT: I 239 CYS cc_start: 0.6972 (t) cc_final: 0.6703 (t) REVERT: I 350 ARG cc_start: 0.8342 (mtt180) cc_final: 0.8124 (mtt180) REVERT: H 21 SER cc_start: 0.8207 (p) cc_final: 0.7971 (t) REVERT: H 53 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8510 (tp) REVERT: H 200 HIS cc_start: 0.7256 (t-170) cc_final: 0.6991 (t-170) REVERT: L 97 THR cc_start: 0.8132 (p) cc_final: 0.7864 (t) outliers start: 59 outliers final: 30 residues processed: 401 average time/residue: 1.2591 time to fit residues: 563.4120 Evaluate side-chains 394 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 360 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 492 GLU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 430 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 165 optimal weight: 0.0270 chunk 144 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 175 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN C 377 ASN C 440 GLN G 103 GLN G 289 ASN G 348 GLN I 85 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.144498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113891 restraints weight = 25436.813| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.74 r_work: 0.3274 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17964 Z= 0.125 Angle : 0.573 9.646 24533 Z= 0.280 Chirality : 0.045 0.271 2951 Planarity : 0.004 0.042 2996 Dihedral : 5.819 57.015 3804 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.36 % Allowed : 19.23 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 0.50 (0.19), residues: 2073 helix: 1.37 (0.29), residues: 384 sheet: 1.30 (0.20), residues: 617 loop : -0.65 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 96 HIS 0.004 0.001 HIS G 374 PHE 0.021 0.001 PHE H 51 TYR 0.016 0.001 TYR C 173 ARG 0.009 0.000 ARG I 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 46) link_NAG-ASN : angle 1.83843 ( 138) link_BETA1-4 : bond 0.00554 ( 24) link_BETA1-4 : angle 1.60760 ( 72) link_ALPHA1-2 : bond 0.00584 ( 1) link_ALPHA1-2 : angle 1.38411 ( 3) link_ALPHA1-3 : bond 0.00911 ( 3) link_ALPHA1-3 : angle 1.13108 ( 9) hydrogen bonds : bond 0.04398 ( 623) hydrogen bonds : angle 4.51818 ( 1788) SS BOND : bond 0.00325 ( 32) SS BOND : angle 1.15263 ( 64) covalent geometry : bond 0.00293 (17858) covalent geometry : angle 0.54838 (24247) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 377 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 LEU cc_start: 0.8610 (tp) cc_final: 0.8395 (mt) REVERT: C 83 GLU cc_start: 0.8082 (tt0) cc_final: 0.7843 (tt0) REVERT: C 123 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8145 (p) REVERT: C 207 LYS cc_start: 0.8259 (pttm) cc_final: 0.8030 (pttm) REVERT: C 217 TYR cc_start: 0.8377 (m-80) cc_final: 0.8144 (m-80) REVERT: C 482 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8029 (mm-30) REVERT: C 502 LYS cc_start: 0.8467 (tttt) cc_final: 0.8218 (tttp) REVERT: F 652 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7913 (mm-40) REVERT: G 116 LEU cc_start: 0.8593 (mt) cc_final: 0.8386 (mt) REVERT: G 153 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7024 (mm-30) REVERT: G 175 LEU cc_start: 0.8378 (mp) cc_final: 0.8136 (mp) REVERT: G 327 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7333 (mtm180) REVERT: G 360 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6048 (ppp80) REVERT: G 419 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7757 (mtp85) REVERT: G 467 THR cc_start: 0.8134 (m) cc_final: 0.7589 (p) REVERT: G 484 TYR cc_start: 0.8567 (p90) cc_final: 0.8339 (p90) REVERT: G 492 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: I 46 LYS cc_start: 0.8064 (mttt) cc_final: 0.7816 (mttt) REVERT: I 113 ASP cc_start: 0.8506 (m-30) cc_final: 0.8284 (m-30) REVERT: I 191 TYR cc_start: 0.8687 (m-80) cc_final: 0.8405 (m-80) REVERT: I 350 ARG cc_start: 0.8392 (mtt180) cc_final: 0.8167 (mtt180) REVERT: H 21 SER cc_start: 0.8217 (p) cc_final: 0.7975 (t) REVERT: H 53 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8488 (tp) REVERT: H 200 HIS cc_start: 0.7269 (t-170) cc_final: 0.6969 (t-170) REVERT: L 24 GLN cc_start: 0.7638 (tt0) cc_final: 0.7306 (tt0) REVERT: L 97 THR cc_start: 0.8173 (p) cc_final: 0.7916 (t) outliers start: 62 outliers final: 38 residues processed: 408 average time/residue: 1.2403 time to fit residues: 565.9787 Evaluate side-chains 408 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 366 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 492 GLU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 500 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 430 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN B 590 GLN C 377 ASN C 440 GLN G 103 GLN G 289 ASN G 348 GLN I 85 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113052 restraints weight = 25294.348| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.74 r_work: 0.3260 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17964 Z= 0.158 Angle : 0.606 9.691 24533 Z= 0.296 Chirality : 0.046 0.281 2951 Planarity : 0.004 0.042 2996 Dihedral : 5.831 57.966 3804 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.30 % Allowed : 19.61 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2073 helix: 1.33 (0.29), residues: 383 sheet: 1.37 (0.20), residues: 603 loop : -0.72 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 112 HIS 0.005 0.001 HIS G 374 PHE 0.024 0.002 PHE H 51 TYR 0.025 0.002 TYR I 173 ARG 0.008 0.001 ARG C 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 46) link_NAG-ASN : angle 1.85834 ( 138) link_BETA1-4 : bond 0.00559 ( 24) link_BETA1-4 : angle 1.63270 ( 72) link_ALPHA1-2 : bond 0.00577 ( 1) link_ALPHA1-2 : angle 1.37255 ( 3) link_ALPHA1-3 : bond 0.00866 ( 3) link_ALPHA1-3 : angle 1.15384 ( 9) hydrogen bonds : bond 0.04866 ( 623) hydrogen bonds : angle 4.57764 ( 1788) SS BOND : bond 0.00364 ( 32) SS BOND : angle 1.39149 ( 64) covalent geometry : bond 0.00383 (17858) covalent geometry : angle 0.58121 (24247) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 367 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8118 (tt0) cc_final: 0.7834 (tt0) REVERT: C 123 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8100 (p) REVERT: C 207 LYS cc_start: 0.8285 (pttm) cc_final: 0.8053 (pttm) REVERT: C 217 TYR cc_start: 0.8391 (m-80) cc_final: 0.8139 (m-80) REVERT: C 482 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7996 (mm-30) REVERT: F 652 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7896 (mm-40) REVERT: G 153 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7119 (mm-30) REVERT: G 175 LEU cc_start: 0.8376 (mp) cc_final: 0.8165 (mp) REVERT: G 215 ILE cc_start: 0.8319 (mt) cc_final: 0.8055 (pt) REVERT: G 289 ASN cc_start: 0.6687 (t0) cc_final: 0.6341 (t0) REVERT: G 327 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7380 (mtm180) REVERT: G 360 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6232 (ppp80) REVERT: G 467 THR cc_start: 0.8147 (m) cc_final: 0.7578 (p) REVERT: G 484 TYR cc_start: 0.8594 (p90) cc_final: 0.8339 (p90) REVERT: G 492 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7883 (mm-30) REVERT: I 46 LYS cc_start: 0.8069 (mttt) cc_final: 0.7830 (mttt) REVERT: I 113 ASP cc_start: 0.8518 (m-30) cc_final: 0.8283 (m-30) REVERT: I 191 TYR cc_start: 0.8704 (m-80) cc_final: 0.8387 (m-80) REVERT: I 239 CYS cc_start: 0.6912 (t) cc_final: 0.6675 (t) REVERT: H 20 LEU cc_start: 0.7893 (mp) cc_final: 0.7660 (mt) REVERT: H 21 SER cc_start: 0.8225 (p) cc_final: 0.7973 (t) REVERT: H 53 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8490 (tp) REVERT: H 200 HIS cc_start: 0.7379 (t-170) cc_final: 0.7035 (t-170) REVERT: L 24 GLN cc_start: 0.7719 (tt0) cc_final: 0.7360 (tt0) REVERT: L 97 THR cc_start: 0.8195 (p) cc_final: 0.7932 (t) outliers start: 61 outliers final: 42 residues processed: 395 average time/residue: 1.2839 time to fit residues: 564.3806 Evaluate side-chains 402 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 356 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 483 LEU Chi-restraints excluded: chain G residue 492 GLU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 430 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain L residue 191 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 110 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN B 577 GLN B 590 GLN C 283 ASN C 377 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 348 GLN I 85 HIS I 136 ASN I 246 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112209 restraints weight = 25147.951| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.73 r_work: 0.3250 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 17964 Z= 0.188 Angle : 0.632 10.825 24533 Z= 0.311 Chirality : 0.046 0.289 2951 Planarity : 0.004 0.043 2996 Dihedral : 5.873 59.016 3804 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.52 % Allowed : 19.61 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2073 helix: 1.30 (0.29), residues: 382 sheet: 1.40 (0.20), residues: 599 loop : -0.75 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 112 HIS 0.006 0.001 HIS G 374 PHE 0.025 0.002 PHE H 51 TYR 0.028 0.002 TYR I 173 ARG 0.009 0.001 ARG I 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 46) link_NAG-ASN : angle 1.92175 ( 138) link_BETA1-4 : bond 0.00539 ( 24) link_BETA1-4 : angle 1.66879 ( 72) link_ALPHA1-2 : bond 0.00558 ( 1) link_ALPHA1-2 : angle 1.37300 ( 3) link_ALPHA1-3 : bond 0.00844 ( 3) link_ALPHA1-3 : angle 1.16616 ( 9) hydrogen bonds : bond 0.05221 ( 623) hydrogen bonds : angle 4.66324 ( 1788) SS BOND : bond 0.00422 ( 32) SS BOND : angle 1.69247 ( 64) covalent geometry : bond 0.00460 (17858) covalent geometry : angle 0.60535 (24247) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 363 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 TRP cc_start: 0.8774 (m100) cc_final: 0.8512 (m100) REVERT: C 123 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8099 (p) REVERT: C 207 LYS cc_start: 0.8230 (pttm) cc_final: 0.7993 (pttm) REVERT: C 217 TYR cc_start: 0.8408 (m-80) cc_final: 0.8193 (m-80) REVERT: C 482 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8025 (mm-30) REVERT: F 652 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7943 (mm-40) REVERT: G 49 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: G 153 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7244 (mm-30) REVERT: G 175 LEU cc_start: 0.8382 (mp) cc_final: 0.8165 (mp) REVERT: G 211 GLU cc_start: 0.7860 (tp30) cc_final: 0.7430 (tp30) REVERT: G 215 ILE cc_start: 0.8348 (mt) cc_final: 0.8094 (pt) REVERT: G 327 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7411 (mtm180) REVERT: G 360 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6355 (ppp80) REVERT: G 393 SER cc_start: 0.8200 (t) cc_final: 0.7921 (m) REVERT: G 419 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7955 (mtp85) REVERT: G 467 THR cc_start: 0.8154 (m) cc_final: 0.7587 (p) REVERT: G 484 TYR cc_start: 0.8614 (p90) cc_final: 0.8379 (p90) REVERT: G 492 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7935 (mm-30) REVERT: I 46 LYS cc_start: 0.8062 (mttt) cc_final: 0.7831 (mttt) REVERT: I 113 ASP cc_start: 0.8509 (m-30) cc_final: 0.8280 (m-30) REVERT: I 191 TYR cc_start: 0.8722 (m-80) cc_final: 0.8421 (m-80) REVERT: I 195 ASN cc_start: 0.8006 (p0) cc_final: 0.7680 (p0) REVERT: I 201 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8148 (mt) REVERT: I 239 CYS cc_start: 0.6931 (t) cc_final: 0.6671 (t) REVERT: H 21 SER cc_start: 0.8266 (p) cc_final: 0.8026 (t) REVERT: H 53 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8512 (tp) REVERT: H 200 HIS cc_start: 0.7444 (t-170) cc_final: 0.7022 (t-170) REVERT: L 33 LEU cc_start: 0.8908 (tt) cc_final: 0.8661 (tp) REVERT: L 97 THR cc_start: 0.8190 (p) cc_final: 0.7925 (t) outliers start: 65 outliers final: 42 residues processed: 391 average time/residue: 1.2720 time to fit residues: 554.3244 Evaluate side-chains 403 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 356 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 183 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 483 LEU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 430 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 135 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 139 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN B 590 GLN C 283 ASN C 377 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 289 ASN G 348 GLN I 85 HIS I 246 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112400 restraints weight = 25122.155| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.73 r_work: 0.3252 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17964 Z= 0.171 Angle : 0.618 9.611 24533 Z= 0.303 Chirality : 0.046 0.283 2951 Planarity : 0.004 0.043 2996 Dihedral : 5.836 59.448 3804 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.25 % Allowed : 20.04 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 0.39 (0.18), residues: 2073 helix: 1.33 (0.29), residues: 383 sheet: 1.29 (0.20), residues: 591 loop : -0.74 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 112 HIS 0.005 0.001 HIS G 374 PHE 0.024 0.002 PHE H 51 TYR 0.027 0.002 TYR I 173 ARG 0.008 0.001 ARG G 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 46) link_NAG-ASN : angle 1.88717 ( 138) link_BETA1-4 : bond 0.00559 ( 24) link_BETA1-4 : angle 1.66371 ( 72) link_ALPHA1-2 : bond 0.00540 ( 1) link_ALPHA1-2 : angle 1.38346 ( 3) link_ALPHA1-3 : bond 0.00823 ( 3) link_ALPHA1-3 : angle 1.18364 ( 9) hydrogen bonds : bond 0.05003 ( 623) hydrogen bonds : angle 4.63515 ( 1788) SS BOND : bond 0.00385 ( 32) SS BOND : angle 1.50169 ( 64) covalent geometry : bond 0.00418 (17858) covalent geometry : angle 0.59283 (24247) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 360 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8079 (tt0) cc_final: 0.7867 (tt0) REVERT: C 96 TRP cc_start: 0.8745 (m100) cc_final: 0.8493 (m100) REVERT: C 123 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8083 (p) REVERT: C 207 LYS cc_start: 0.8241 (pttm) cc_final: 0.7986 (pttm) REVERT: C 482 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8036 (mm-30) REVERT: F 652 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7953 (mm-40) REVERT: G 151 ARG cc_start: 0.8322 (mtt90) cc_final: 0.8006 (ttm-80) REVERT: G 153 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7188 (mm-30) REVERT: G 175 LEU cc_start: 0.8376 (mp) cc_final: 0.8167 (mp) REVERT: G 211 GLU cc_start: 0.7869 (tp30) cc_final: 0.7450 (tp30) REVERT: G 215 ILE cc_start: 0.8338 (mt) cc_final: 0.8098 (pt) REVERT: G 289 ASN cc_start: 0.6654 (t0) cc_final: 0.6408 (t0) REVERT: G 327 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7385 (mtm180) REVERT: G 360 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6417 (ppp80) REVERT: G 393 SER cc_start: 0.8176 (t) cc_final: 0.7906 (m) REVERT: G 419 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7937 (mtp85) REVERT: G 484 TYR cc_start: 0.8621 (p90) cc_final: 0.8352 (p90) REVERT: G 492 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7935 (mm-30) REVERT: I 46 LYS cc_start: 0.8056 (mttt) cc_final: 0.7805 (mttt) REVERT: I 113 ASP cc_start: 0.8501 (m-30) cc_final: 0.8273 (m-30) REVERT: I 195 ASN cc_start: 0.8089 (p0) cc_final: 0.7773 (p0) REVERT: I 201 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8150 (mt) REVERT: I 239 CYS cc_start: 0.6856 (t) cc_final: 0.6606 (t) REVERT: H 21 SER cc_start: 0.8276 (p) cc_final: 0.8032 (t) REVERT: H 53 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8490 (tp) REVERT: L 24 GLN cc_start: 0.7723 (tt0) cc_final: 0.7413 (tt0) REVERT: L 33 LEU cc_start: 0.8916 (tt) cc_final: 0.8675 (tp) REVERT: L 69 THR cc_start: 0.8129 (p) cc_final: 0.7846 (m) REVERT: L 79 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6804 (mm110) REVERT: L 97 THR cc_start: 0.8201 (p) cc_final: 0.7919 (t) outliers start: 60 outliers final: 44 residues processed: 391 average time/residue: 1.2853 time to fit residues: 562.6522 Evaluate side-chains 401 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 352 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 183 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 483 LEU Chi-restraints excluded: chain G residue 492 GLU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 430 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 7 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN B 590 GLN C 283 ASN C 377 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN G 348 GLN I 85 HIS I 136 ASN I 246 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112805 restraints weight = 25171.721| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.74 r_work: 0.3263 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17964 Z= 0.147 Angle : 0.601 10.819 24533 Z= 0.293 Chirality : 0.045 0.273 2951 Planarity : 0.004 0.042 2996 Dihedral : 5.753 59.402 3804 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.20 % Allowed : 20.15 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 0.45 (0.18), residues: 2073 helix: 1.43 (0.29), residues: 383 sheet: 1.31 (0.20), residues: 605 loop : -0.73 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 35 HIS 0.004 0.001 HIS G 374 PHE 0.022 0.002 PHE H 51 TYR 0.025 0.001 TYR I 173 ARG 0.008 0.001 ARG I 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 46) link_NAG-ASN : angle 1.81959 ( 138) link_BETA1-4 : bond 0.00572 ( 24) link_BETA1-4 : angle 1.64990 ( 72) link_ALPHA1-2 : bond 0.00527 ( 1) link_ALPHA1-2 : angle 1.39636 ( 3) link_ALPHA1-3 : bond 0.00784 ( 3) link_ALPHA1-3 : angle 1.20137 ( 9) hydrogen bonds : bond 0.04684 ( 623) hydrogen bonds : angle 4.56685 ( 1788) SS BOND : bond 0.00336 ( 32) SS BOND : angle 1.37716 ( 64) covalent geometry : bond 0.00354 (17858) covalent geometry : angle 0.57684 (24247) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 357 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8084 (tt0) cc_final: 0.7860 (tt0) REVERT: C 96 TRP cc_start: 0.8742 (m100) cc_final: 0.8484 (m100) REVERT: C 123 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8064 (p) REVERT: C 207 LYS cc_start: 0.8212 (pttm) cc_final: 0.7956 (pttm) REVERT: C 482 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8054 (mm-30) REVERT: F 652 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7931 (mm-40) REVERT: G 151 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7957 (ttm-80) REVERT: G 153 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7256 (mm-30) REVERT: G 175 LEU cc_start: 0.8380 (mp) cc_final: 0.8157 (mp) REVERT: G 211 GLU cc_start: 0.7858 (tp30) cc_final: 0.7444 (tp30) REVERT: G 215 ILE cc_start: 0.8349 (mt) cc_final: 0.8111 (pt) REVERT: G 327 ARG cc_start: 0.7798 (mtm110) cc_final: 0.7426 (mtm180) REVERT: G 360 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6384 (ppp80) REVERT: G 393 SER cc_start: 0.8168 (OUTLIER) cc_final: 0.7892 (m) REVERT: G 419 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7923 (mtp85) REVERT: G 484 TYR cc_start: 0.8594 (p90) cc_final: 0.8360 (p90) REVERT: G 492 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: I 46 LYS cc_start: 0.8053 (mttt) cc_final: 0.7827 (mttt) REVERT: I 113 ASP cc_start: 0.8494 (m-30) cc_final: 0.8281 (m-30) REVERT: I 166 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7591 (ttp-170) REVERT: I 195 ASN cc_start: 0.8069 (p0) cc_final: 0.7760 (p0) REVERT: I 201 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8148 (mt) REVERT: I 239 CYS cc_start: 0.6814 (t) cc_final: 0.6572 (t) REVERT: H 21 SER cc_start: 0.8276 (p) cc_final: 0.8026 (t) REVERT: H 53 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8512 (tp) REVERT: L 24 GLN cc_start: 0.7697 (tt0) cc_final: 0.7414 (tt0) REVERT: L 33 LEU cc_start: 0.8912 (tt) cc_final: 0.8671 (tp) REVERT: L 69 THR cc_start: 0.8140 (p) cc_final: 0.7867 (m) REVERT: L 79 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6796 (mm-40) outliers start: 59 outliers final: 44 residues processed: 385 average time/residue: 1.3276 time to fit residues: 568.8404 Evaluate side-chains 409 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 359 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 183 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 483 LEU Chi-restraints excluded: chain G residue 492 GLU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 430 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 172 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 chunk 198 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN B 590 GLN C 283 ASN C 377 ASN F 653 GLN G 103 GLN G 289 ASN I 85 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.141938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111897 restraints weight = 25098.786| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.72 r_work: 0.3254 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17964 Z= 0.189 Angle : 0.643 9.708 24533 Z= 0.315 Chirality : 0.046 0.285 2951 Planarity : 0.004 0.042 2996 Dihedral : 5.849 59.612 3804 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.14 % Allowed : 20.53 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 0.38 (0.18), residues: 2073 helix: 1.31 (0.29), residues: 383 sheet: 1.33 (0.20), residues: 588 loop : -0.75 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 35 HIS 0.006 0.001 HIS G 374 PHE 0.026 0.002 PHE H 51 TYR 0.027 0.002 TYR I 173 ARG 0.008 0.001 ARG I 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 46) link_NAG-ASN : angle 1.92568 ( 138) link_BETA1-4 : bond 0.00562 ( 24) link_BETA1-4 : angle 1.68269 ( 72) link_ALPHA1-2 : bond 0.00511 ( 1) link_ALPHA1-2 : angle 1.39321 ( 3) link_ALPHA1-3 : bond 0.00786 ( 3) link_ALPHA1-3 : angle 1.20550 ( 9) hydrogen bonds : bond 0.05283 ( 623) hydrogen bonds : angle 4.68422 ( 1788) SS BOND : bond 0.00412 ( 32) SS BOND : angle 1.61600 ( 64) covalent geometry : bond 0.00463 (17858) covalent geometry : angle 0.61696 (24247) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 346 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8045 (tt0) cc_final: 0.7797 (tt0) REVERT: C 96 TRP cc_start: 0.8755 (m100) cc_final: 0.8497 (m100) REVERT: C 123 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8076 (p) REVERT: C 207 LYS cc_start: 0.8221 (pttm) cc_final: 0.7955 (pttm) REVERT: C 482 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7996 (mm-30) REVERT: F 652 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7898 (mm-40) REVERT: G 95 MET cc_start: 0.8493 (ttm) cc_final: 0.8273 (ttm) REVERT: G 151 ARG cc_start: 0.8308 (mtt90) cc_final: 0.8003 (ttm-80) REVERT: G 153 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7255 (mm-30) REVERT: G 211 GLU cc_start: 0.7846 (tp30) cc_final: 0.7415 (tp30) REVERT: G 215 ILE cc_start: 0.8376 (mt) cc_final: 0.8130 (pt) REVERT: G 289 ASN cc_start: 0.6705 (t0) cc_final: 0.6501 (t0) REVERT: G 327 ARG cc_start: 0.7802 (mtm110) cc_final: 0.7445 (mtm180) REVERT: G 360 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6492 (ppp80) REVERT: G 393 SER cc_start: 0.8207 (OUTLIER) cc_final: 0.7933 (m) REVERT: G 419 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7960 (mtp85) REVERT: G 492 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7923 (mm-30) REVERT: I 46 LYS cc_start: 0.8109 (mttt) cc_final: 0.7885 (mttt) REVERT: I 195 ASN cc_start: 0.8104 (p0) cc_final: 0.7791 (p0) REVERT: I 201 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8102 (mt) REVERT: I 239 CYS cc_start: 0.6856 (t) cc_final: 0.6619 (t) REVERT: H 21 SER cc_start: 0.8291 (p) cc_final: 0.8037 (t) REVERT: H 53 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8527 (tp) REVERT: L 20 THR cc_start: 0.8381 (p) cc_final: 0.8106 (m) REVERT: L 24 GLN cc_start: 0.7780 (tt0) cc_final: 0.7430 (tt0) REVERT: L 33 LEU cc_start: 0.8913 (tt) cc_final: 0.8684 (tp) REVERT: L 69 THR cc_start: 0.8110 (p) cc_final: 0.7858 (m) REVERT: L 79 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6901 (mm-40) outliers start: 58 outliers final: 44 residues processed: 377 average time/residue: 1.3843 time to fit residues: 580.6114 Evaluate side-chains 402 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 352 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 183 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 393 SER Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 483 LEU Chi-restraints excluded: chain G residue 492 GLU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 430 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 103 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 63 optimal weight: 0.0270 chunk 171 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 116 optimal weight: 0.0770 chunk 149 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN B 590 GLN C 283 ASN C 377 ASN G 103 GLN I 85 HIS I 136 ASN H 39 GLN L 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.143385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113291 restraints weight = 25111.889| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.73 r_work: 0.3267 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17964 Z= 0.120 Angle : 0.586 9.482 24533 Z= 0.286 Chirality : 0.044 0.262 2951 Planarity : 0.004 0.042 2996 Dihedral : 5.682 58.693 3804 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.65 % Allowed : 21.07 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: 0.49 (0.18), residues: 2073 helix: 1.45 (0.29), residues: 388 sheet: 1.34 (0.20), residues: 602 loop : -0.71 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 35 HIS 0.003 0.001 HIS G 374 PHE 0.019 0.001 PHE H 51 TYR 0.024 0.001 TYR I 173 ARG 0.009 0.000 ARG I 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 46) link_NAG-ASN : angle 1.76760 ( 138) link_BETA1-4 : bond 0.00569 ( 24) link_BETA1-4 : angle 1.62810 ( 72) link_ALPHA1-2 : bond 0.00513 ( 1) link_ALPHA1-2 : angle 1.40904 ( 3) link_ALPHA1-3 : bond 0.00761 ( 3) link_ALPHA1-3 : angle 1.22295 ( 9) hydrogen bonds : bond 0.04332 ( 623) hydrogen bonds : angle 4.50525 ( 1788) SS BOND : bond 0.00300 ( 32) SS BOND : angle 1.33362 ( 64) covalent geometry : bond 0.00282 (17858) covalent geometry : angle 0.56235 (24247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15211.97 seconds wall clock time: 262 minutes 16.90 seconds (15736.90 seconds total)