Starting phenix.real_space_refine on Mon Mar 18 21:56:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b7n_7063/03_2024/6b7n_7063.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b7n_7063/03_2024/6b7n_7063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b7n_7063/03_2024/6b7n_7063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b7n_7063/03_2024/6b7n_7063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b7n_7063/03_2024/6b7n_7063.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b7n_7063/03_2024/6b7n_7063.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 14019 2.51 5 N 3609 2.21 5 O 4467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22215 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7139 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 33, 'TRANS': 932} Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 2, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 19, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 242 Chain: "B" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7139 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 33, 'TRANS': 932} Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 2, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 19, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 242 Chain: "C" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7139 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 33, 'TRANS': 932} Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 2, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 19, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 242 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 11.77, per 1000 atoms: 0.53 Number of scatterers: 22215 At special positions: 0 Unit cell: (124.8, 119.6, 150.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4467 8.00 N 3609 7.00 C 14019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.04 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 532 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.02 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 710 " distance=2.03 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 912 " distance=2.04 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 997 " distance=2.04 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 352 " distance=2.04 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 608 " distance=2.02 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 710 " distance=2.03 Simple disulfide: pdb=" SG CYS B 901 " - pdb=" SG CYS B 912 " distance=2.04 Simple disulfide: pdb=" SG CYS B 951 " - pdb=" SG CYS B 997 " distance=2.04 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 378 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 352 " distance=2.04 Simple disulfide: pdb=" SG CYS C 361 " - pdb=" SG CYS C 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 545 " distance=2.02 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 608 " distance=2.02 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 710 " distance=2.03 Simple disulfide: pdb=" SG CYS C 901 " - pdb=" SG CYS C 912 " distance=2.04 Simple disulfide: pdb=" SG CYS C 951 " - pdb=" SG CYS C 997 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " " 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 Q 2 " - " NAG Q 3 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1205 " - " ASN A 184 " " NAG A1206 " - " ASN A 162 " " NAG A1207 " - " ASN A 251 " " NAG A1208 " - " ASN A 311 " " NAG A1209 " - " ASN A 472 " " NAG A1210 " - " ASN A 494 " " NAG A1211 " - " ASN A 661 " " NAG A1217 " - " ASN A1003 " " NAG B1205 " - " ASN B 184 " " NAG B1206 " - " ASN B 162 " " NAG B1207 " - " ASN B 251 " " NAG B1208 " - " ASN B 311 " " NAG B1209 " - " ASN B 472 " " NAG B1210 " - " ASN B 494 " " NAG B1211 " - " ASN B 661 " " NAG B1217 " - " ASN B1003 " " NAG C1205 " - " ASN C 184 " " NAG C1206 " - " ASN C 162 " " NAG C1207 " - " ASN C 251 " " NAG C1208 " - " ASN C 311 " " NAG C1209 " - " ASN C 472 " " NAG C1210 " - " ASN C 494 " " NAG C1211 " - " ASN C 661 " " NAG C1217 " - " ASN C1003 " " NAG D 1 " - " ASN A 241 " " NAG E 1 " - " ASN A 74 " " NAG F 1 " - " ASN A 788 " " NAG G 1 " - " ASN A 914 " " NAG H 1 " - " ASN A 526 " " NAG I 1 " - " ASN B 241 " " NAG J 1 " - " ASN B 74 " " NAG K 1 " - " ASN B 788 " " NAG L 1 " - " ASN B 914 " " NAG M 1 " - " ASN B 526 " " NAG N 1 " - " ASN C 241 " " NAG O 1 " - " ASN C 74 " " NAG P 1 " - " ASN C 788 " " NAG Q 1 " - " ASN C 914 " " NAG R 1 " - " ASN C 526 " Time building additional restraints: 9.40 Conformation dependent library (CDL) restraints added in 4.1 seconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 27.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 117 through 123 removed outlier: 4.263A pdb=" N VAL A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.565A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.846A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 605 through 615 removed outlier: 3.725A pdb=" N TYR A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 641 Processing helix chain 'A' and resid 644 through 650 Processing helix chain 'A' and resid 651 through 657 removed outlier: 6.126A pdb=" N THR A 654 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 657 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 695 through 699 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 795 Processing helix chain 'A' and resid 805 through 835 removed outlier: 3.744A pdb=" N VAL A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 854 through 902 removed outlier: 3.611A pdb=" N ALA A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 902 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 991 removed outlier: 3.981A pdb=" N ASP A 990 " --> pdb=" O ARG A 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 991 " --> pdb=" O GLN A 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 991' Processing helix chain 'A' and resid 1008 through 1013 Processing helix chain 'B' and resid 117 through 123 removed outlier: 4.263A pdb=" N VAL B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.566A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.844A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 371' Processing helix chain 'B' and resid 596 through 602 Processing helix chain 'B' and resid 605 through 615 removed outlier: 3.726A pdb=" N TYR B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 641 Processing helix chain 'B' and resid 644 through 650 Processing helix chain 'B' and resid 651 through 657 removed outlier: 6.125A pdb=" N THR B 654 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 657 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 682 Processing helix chain 'B' and resid 695 through 699 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 725 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 752 through 765 Processing helix chain 'B' and resid 774 through 795 Processing helix chain 'B' and resid 805 through 835 removed outlier: 3.743A pdb=" N VAL B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 812 " --> pdb=" O ASN B 808 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN B 824 " --> pdb=" O VAL B 820 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B 828 " --> pdb=" O GLN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 851 Processing helix chain 'B' and resid 854 through 902 removed outlier: 3.610A pdb=" N ALA B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 902 " --> pdb=" O ILE B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 991 removed outlier: 3.982A pdb=" N ASP B 990 " --> pdb=" O ARG B 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 991 " --> pdb=" O GLN B 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 987 through 991' Processing helix chain 'B' and resid 1008 through 1013 Processing helix chain 'C' and resid 117 through 123 removed outlier: 4.264A pdb=" N VAL C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 122 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 263 through 273 removed outlier: 3.566A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.844A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 596 through 602 Processing helix chain 'C' and resid 605 through 615 removed outlier: 3.725A pdb=" N TYR C 615 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 641 Processing helix chain 'C' and resid 644 through 650 Processing helix chain 'C' and resid 651 through 657 removed outlier: 6.125A pdb=" N THR C 654 " --> pdb=" O ALA C 651 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 657 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 682 Processing helix chain 'C' and resid 695 through 699 Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 725 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 752 through 765 Processing helix chain 'C' and resid 774 through 795 Processing helix chain 'C' and resid 805 through 835 removed outlier: 3.744A pdb=" N VAL C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 812 " --> pdb=" O ASN C 808 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY C 825 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA C 827 " --> pdb=" O GLN C 823 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU C 828 " --> pdb=" O GLN C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 851 Processing helix chain 'C' and resid 854 through 902 removed outlier: 3.609A pdb=" N ALA C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 902 " --> pdb=" O ILE C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 991 removed outlier: 3.980A pdb=" N ASP C 990 " --> pdb=" O ARG C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 991 " --> pdb=" O GLN C 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 987 through 991' Processing helix chain 'C' and resid 1008 through 1013 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 85 removed outlier: 6.204A pdb=" N THR A 250 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.556A pdb=" N PHE A 237 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 4.472A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 105 removed outlier: 3.677A pdb=" N LEU A 225 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 143 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY A 189 " --> pdb=" O CYS A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 281 through 282 removed outlier: 6.441A pdb=" N GLN A 489 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA A 500 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 491 " --> pdb=" O VAL A 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 297 removed outlier: 3.632A pdb=" N THR A 434 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR A 468 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 462 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU A 467 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 460 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.603A pdb=" N GLU A 344 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 372 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 335 removed outlier: 3.513A pdb=" N CYS A 386 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.526A pdb=" N THR A 353 " --> pdb=" O THR A 393 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.815A pdb=" N LEU A 537 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 569 through 574 Processing sheet with id=AB3, first strand: chain 'A' and resid 580 through 587 removed outlier: 3.613A pdb=" N VAL A 935 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 928 " --> pdb=" O ALA A 925 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AB5, first strand: chain 'A' and resid 949 through 952 Processing sheet with id=AB6, first strand: chain 'A' and resid 964 through 969 Processing sheet with id=AB7, first strand: chain 'B' and resid 80 through 85 removed outlier: 6.205A pdb=" N THR B 250 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.555A pdb=" N PHE B 237 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 91 removed outlier: 4.472A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N PHE B 206 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 105 removed outlier: 3.677A pdb=" N LEU B 225 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 143 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 189 " --> pdb=" O CYS B 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 281 through 282 removed outlier: 6.443A pdb=" N GLN B 489 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA B 500 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 491 " --> pdb=" O VAL B 498 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 296 through 297 removed outlier: 3.631A pdb=" N THR B 434 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR B 468 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 462 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 467 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE B 460 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.602A pdb=" N GLU B 344 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B 372 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 333 through 335 removed outlier: 3.514A pdb=" N CYS B 386 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 353 through 356 removed outlier: 3.525A pdb=" N THR B 353 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 539 removed outlier: 3.815A pdb=" N LEU B 537 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 569 through 574 Processing sheet with id=AC9, first strand: chain 'B' and resid 580 through 587 removed outlier: 3.612A pdb=" N VAL B 935 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 928 " --> pdb=" O ALA B 925 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 593 through 595 Processing sheet with id=AD2, first strand: chain 'B' and resid 949 through 952 Processing sheet with id=AD3, first strand: chain 'B' and resid 964 through 969 Processing sheet with id=AD4, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.203A pdb=" N THR C 250 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.556A pdb=" N PHE C 237 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 91 removed outlier: 4.472A pdb=" N GLN C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE C 206 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.676A pdb=" N LEU C 225 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 143 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY C 189 " --> pdb=" O CYS C 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 281 through 282 removed outlier: 6.442A pdb=" N GLN C 489 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA C 500 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE C 491 " --> pdb=" O VAL C 498 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.633A pdb=" N THR C 434 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR C 468 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER C 462 " --> pdb=" O GLY C 465 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU C 467 " --> pdb=" O PHE C 460 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE C 460 " --> pdb=" O LEU C 467 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.603A pdb=" N GLU C 344 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C 372 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 333 through 335 removed outlier: 3.514A pdb=" N CYS C 386 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 353 through 356 removed outlier: 3.526A pdb=" N THR C 353 " --> pdb=" O THR C 393 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.816A pdb=" N LEU C 537 " --> pdb=" O VAL C 544 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 569 through 574 Processing sheet with id=AE6, first strand: chain 'C' and resid 580 through 587 removed outlier: 3.612A pdb=" N VAL C 935 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 928 " --> pdb=" O ALA C 925 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 593 through 595 Processing sheet with id=AE8, first strand: chain 'C' and resid 949 through 952 Processing sheet with id=AE9, first strand: chain 'C' and resid 964 through 969 888 hydrogen bonds defined for protein. 2439 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: 9.15 Time building geometry restraints manager: 10.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6630 1.33 - 1.46: 5433 1.46 - 1.58: 10383 1.58 - 1.71: 0 1.71 - 1.83: 162 Bond restraints: 22608 Sorted by residual: bond pdb=" C1 NAG L 3 " pdb=" O5 NAG L 3 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C1 NAG G 3 " pdb=" O5 NAG G 3 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C1 NAG Q 3 " pdb=" O5 NAG Q 3 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C1 NAG B1210 " pdb=" O5 NAG B1210 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.55e+00 bond pdb=" CA PRO A 192 " pdb=" C PRO A 192 " ideal model delta sigma weight residual 1.517 1.501 0.016 6.70e-03 2.23e+04 5.48e+00 ... (remaining 22603 not shown) Histogram of bond angle deviations from ideal: 98.69 - 106.55: 610 106.55 - 114.42: 13892 114.42 - 122.29: 12714 122.29 - 130.15: 3645 130.15 - 138.02: 99 Bond angle restraints: 30960 Sorted by residual: angle pdb=" CA LEU B 467 " pdb=" CB LEU B 467 " pdb=" CG LEU B 467 " ideal model delta sigma weight residual 116.30 138.02 -21.72 3.50e+00 8.16e-02 3.85e+01 angle pdb=" CA LEU A 467 " pdb=" CB LEU A 467 " pdb=" CG LEU A 467 " ideal model delta sigma weight residual 116.30 138.00 -21.70 3.50e+00 8.16e-02 3.85e+01 angle pdb=" CA LEU C 467 " pdb=" CB LEU C 467 " pdb=" CG LEU C 467 " ideal model delta sigma weight residual 116.30 137.98 -21.68 3.50e+00 8.16e-02 3.84e+01 angle pdb=" C LEU B 994 " pdb=" N THR B 995 " pdb=" CA THR B 995 " ideal model delta sigma weight residual 121.54 133.31 -11.77 1.91e+00 2.74e-01 3.80e+01 angle pdb=" C LEU A 994 " pdb=" N THR A 995 " pdb=" CA THR A 995 " ideal model delta sigma weight residual 121.54 133.30 -11.76 1.91e+00 2.74e-01 3.79e+01 ... (remaining 30955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 13446 17.80 - 35.60: 562 35.60 - 53.40: 173 53.40 - 71.21: 27 71.21 - 89.01: 18 Dihedral angle restraints: 14226 sinusoidal: 5724 harmonic: 8502 Sorted by residual: dihedral pdb=" CA LEU A 556 " pdb=" C LEU A 556 " pdb=" N GLN A 557 " pdb=" CA GLN A 557 " ideal model delta harmonic sigma weight residual 180.00 126.53 53.47 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA LEU B 556 " pdb=" C LEU B 556 " pdb=" N GLN B 557 " pdb=" CA GLN B 557 " ideal model delta harmonic sigma weight residual 180.00 126.55 53.45 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA LEU C 556 " pdb=" C LEU C 556 " pdb=" N GLN C 557 " pdb=" CA GLN C 557 " ideal model delta harmonic sigma weight residual 180.00 126.60 53.40 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 14223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 3793 0.118 - 0.236: 178 0.236 - 0.355: 25 0.355 - 0.473: 6 0.473 - 0.591: 6 Chirality restraints: 4008 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 526 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.73e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 526 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.95e+00 chirality pdb=" C1 NAG A1217 " pdb=" ND2 ASN A1003 " pdb=" C2 NAG A1217 " pdb=" O5 NAG A1217 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.87e+00 ... (remaining 4005 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 358 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C THR A 358 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 358 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 359 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 358 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C THR B 358 " 0.057 2.00e-02 2.50e+03 pdb=" O THR B 358 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP B 359 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 358 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C THR C 358 " 0.057 2.00e-02 2.50e+03 pdb=" O THR C 358 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP C 359 " -0.019 2.00e-02 2.50e+03 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1365 2.72 - 3.26: 22344 3.26 - 3.81: 36242 3.81 - 4.35: 42158 4.35 - 4.90: 72173 Nonbonded interactions: 174282 Sorted by model distance: nonbonded pdb=" OG SER B 442 " pdb=" OD1 ASP C 848 " model vdw 2.171 2.440 nonbonded pdb=" OG SER C 462 " pdb=" O GLY C 465 " model vdw 2.191 2.440 nonbonded pdb=" OG SER B 462 " pdb=" O GLY B 465 " model vdw 2.192 2.440 nonbonded pdb=" OG SER A 462 " pdb=" O GLY A 465 " model vdw 2.193 2.440 nonbonded pdb=" OG SER A 959 " pdb=" OG1 THR B 768 " model vdw 2.215 2.440 ... (remaining 174277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.900 Check model and map are aligned: 0.290 Set scattering table: 0.220 Process input model: 61.070 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.008 0.130 22608 Z= 0.554 Angle : 1.139 21.719 30960 Z= 0.586 Chirality : 0.066 0.591 4008 Planarity : 0.008 0.073 3873 Dihedral : 11.304 77.905 8625 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.07 % Favored : 87.52 % Rotamer: Outliers : 0.78 % Allowed : 4.02 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -4.33 (0.13), residues: 2892 helix: -2.00 (0.15), residues: 684 sheet: -2.86 (0.19), residues: 588 loop : -3.39 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP A 973 HIS 0.011 0.004 HIS A 126 PHE 0.038 0.004 PHE B 839 TYR 0.038 0.003 TYR B 226 ARG 0.009 0.001 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 2.098 Fit side-chains REVERT: A 218 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8938 (tp) REVERT: A 731 MET cc_start: 0.8826 (mtm) cc_final: 0.8588 (mtm) REVERT: B 731 MET cc_start: 0.8699 (mtm) cc_final: 0.8404 (mtm) REVERT: C 104 MET cc_start: 0.8437 (ptp) cc_final: 0.8127 (ptp) REVERT: C 372 MET cc_start: 0.8224 (tpp) cc_final: 0.7981 (tpp) outliers start: 18 outliers final: 1 residues processed: 101 average time/residue: 0.3367 time to fit residues: 55.1747 Evaluate side-chains 56 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain B residue 365 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 chunk 147 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 87 GLN ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN A 402 GLN A 489 GLN A 557 GLN A 639 ASN A 847 GLN A 895 GLN A 939 ASN A 968 GLN A1011 ASN B 65 ASN B 87 GLN ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN B 402 GLN B 557 GLN B 847 GLN B 895 GLN B 939 ASN B 968 GLN B1011 ASN C 65 ASN C 87 GLN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 402 GLN C 557 GLN C 639 ASN C 847 GLN C 895 GLN C 939 ASN C 968 GLN C1011 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22608 Z= 0.197 Angle : 0.757 18.486 30960 Z= 0.381 Chirality : 0.047 0.434 4008 Planarity : 0.005 0.053 3873 Dihedral : 9.178 59.263 4279 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.37 % Favored : 89.21 % Rotamer: Outliers : 1.47 % Allowed : 6.61 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -3.08 (0.15), residues: 2892 helix: 0.40 (0.19), residues: 678 sheet: -2.78 (0.20), residues: 537 loop : -2.99 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 973 HIS 0.004 0.001 HIS C 421 PHE 0.015 0.002 PHE B 839 TYR 0.021 0.001 TYR A 226 ARG 0.009 0.001 ARG B 888 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 60 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8961 (tp) REVERT: B 731 MET cc_start: 0.8785 (mtm) cc_final: 0.8519 (mtm) REVERT: C 718 MET cc_start: 0.8141 (mtp) cc_final: 0.7822 (mtm) outliers start: 34 outliers final: 14 residues processed: 94 average time/residue: 0.2850 time to fit residues: 47.4480 Evaluate side-chains 67 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 217 optimal weight: 0.0170 chunk 178 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 767 GLN ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN B 767 GLN C 126 HIS C 767 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22608 Z= 0.281 Angle : 0.736 12.178 30960 Z= 0.368 Chirality : 0.047 0.431 4008 Planarity : 0.004 0.047 3873 Dihedral : 8.276 59.854 4279 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.03 % Favored : 87.55 % Rotamer: Outliers : 2.03 % Allowed : 7.87 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.45 (0.16), residues: 2892 helix: 1.53 (0.20), residues: 678 sheet: -2.33 (0.19), residues: 612 loop : -2.89 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 973 HIS 0.006 0.002 HIS A 421 PHE 0.023 0.002 PHE B 577 TYR 0.025 0.002 TYR B 226 ARG 0.010 0.000 ARG C 888 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 52 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8966 (tp) REVERT: A 358 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7199 (m) REVERT: A 771 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 358 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7445 (m) REVERT: B 718 MET cc_start: 0.8136 (mtp) cc_final: 0.7784 (mtm) REVERT: B 731 MET cc_start: 0.8864 (mtm) cc_final: 0.8636 (mtm) REVERT: C 718 MET cc_start: 0.8179 (mtp) cc_final: 0.7839 (mtm) outliers start: 47 outliers final: 28 residues processed: 97 average time/residue: 0.2530 time to fit residues: 44.8559 Evaluate side-chains 83 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 51 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22608 Z= 0.214 Angle : 0.683 14.377 30960 Z= 0.339 Chirality : 0.045 0.433 4008 Planarity : 0.004 0.045 3873 Dihedral : 7.758 59.046 4279 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.34 % Favored : 88.24 % Rotamer: Outliers : 2.81 % Allowed : 8.52 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.13 (0.16), residues: 2892 helix: 2.09 (0.20), residues: 675 sheet: -2.20 (0.20), residues: 603 loop : -2.80 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 973 HIS 0.006 0.001 HIS A 236 PHE 0.023 0.002 PHE C 839 TYR 0.020 0.001 TYR C 226 ARG 0.002 0.000 ARG C 888 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 51 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8980 (m) REVERT: A 980 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7344 (mtm) REVERT: B 718 MET cc_start: 0.8153 (mtp) cc_final: 0.7809 (mtm) REVERT: C 372 MET cc_start: 0.8539 (ttm) cc_final: 0.8041 (ttm) REVERT: C 391 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9091 (pt) REVERT: C 718 MET cc_start: 0.8191 (mtp) cc_final: 0.7738 (mtm) outliers start: 65 outliers final: 36 residues processed: 111 average time/residue: 0.2500 time to fit residues: 50.6856 Evaluate side-chains 90 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 51 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 237 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 22608 Z= 0.408 Angle : 0.778 14.672 30960 Z= 0.387 Chirality : 0.047 0.454 4008 Planarity : 0.004 0.047 3873 Dihedral : 8.020 56.079 4277 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.62 % Favored : 86.96 % Rotamer: Outliers : 3.29 % Allowed : 9.38 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -2.06 (0.16), residues: 2892 helix: 2.18 (0.20), residues: 675 sheet: -2.22 (0.20), residues: 582 loop : -2.75 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 973 HIS 0.009 0.002 HIS C 236 PHE 0.025 0.002 PHE C 839 TYR 0.027 0.002 TYR B 226 ARG 0.004 0.001 ARG A 978 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 51 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9126 (pp) REVERT: A 316 MET cc_start: 0.8481 (mtp) cc_final: 0.8203 (mtp) REVERT: A 372 MET cc_start: 0.8988 (ttm) cc_final: 0.8627 (ttm) REVERT: A 980 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7493 (mtm) REVERT: B 86 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: B 516 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8840 (mp) REVERT: C 372 MET cc_start: 0.8521 (ttm) cc_final: 0.8061 (ttm) REVERT: C 718 MET cc_start: 0.8271 (mtp) cc_final: 0.7813 (mtm) REVERT: C 731 MET cc_start: 0.8948 (mtm) cc_final: 0.8540 (ttm) outliers start: 76 outliers final: 49 residues processed: 117 average time/residue: 0.2511 time to fit residues: 52.8434 Evaluate side-chains 104 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 51 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 930 PHE Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 92 optimal weight: 0.0870 chunk 146 optimal weight: 6.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22608 Z= 0.165 Angle : 0.668 11.879 30960 Z= 0.331 Chirality : 0.045 0.432 4008 Planarity : 0.004 0.045 3873 Dihedral : 7.341 59.817 4277 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.68 % Favored : 88.90 % Rotamer: Outliers : 2.29 % Allowed : 10.94 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -1.85 (0.16), residues: 2892 helix: 2.47 (0.20), residues: 675 sheet: -2.02 (0.21), residues: 567 loop : -2.70 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 973 HIS 0.005 0.001 HIS A 421 PHE 0.021 0.002 PHE C 839 TYR 0.014 0.001 TYR A 226 ARG 0.003 0.000 ARG C 888 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 54 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9073 (pp) REVERT: A 316 MET cc_start: 0.8417 (mtp) cc_final: 0.8186 (mtp) REVERT: A 980 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7551 (mtm) REVERT: B 86 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8490 (m-80) REVERT: B 718 MET cc_start: 0.8197 (mtp) cc_final: 0.7873 (mtm) REVERT: C 372 MET cc_start: 0.8524 (ttm) cc_final: 0.8057 (ttm) REVERT: C 718 MET cc_start: 0.8244 (mtp) cc_final: 0.7782 (mtm) outliers start: 53 outliers final: 32 residues processed: 99 average time/residue: 0.2556 time to fit residues: 46.2148 Evaluate side-chains 86 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 51 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22608 Z= 0.243 Angle : 0.677 11.684 30960 Z= 0.335 Chirality : 0.045 0.435 4008 Planarity : 0.004 0.045 3873 Dihedral : 7.224 59.995 4275 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.38 % Favored : 88.21 % Rotamer: Outliers : 2.55 % Allowed : 10.98 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -1.76 (0.16), residues: 2892 helix: 2.59 (0.20), residues: 675 sheet: -2.00 (0.21), residues: 558 loop : -2.65 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 973 HIS 0.006 0.001 HIS A 421 PHE 0.032 0.002 PHE B 577 TYR 0.018 0.001 TYR B 226 ARG 0.002 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 51 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7752 (p0) REVERT: A 249 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9076 (pp) REVERT: A 316 MET cc_start: 0.8463 (mtp) cc_final: 0.8246 (mtp) REVERT: A 980 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7610 (mtm) REVERT: B 86 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8517 (m-80) REVERT: B 718 MET cc_start: 0.8230 (mtp) cc_final: 0.7898 (mtm) REVERT: B 930 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.6892 (p90) REVERT: C 372 MET cc_start: 0.8534 (ttm) cc_final: 0.8084 (ttm) REVERT: C 388 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.8680 (mtp) REVERT: C 718 MET cc_start: 0.8284 (mtp) cc_final: 0.7816 (mtm) REVERT: C 731 MET cc_start: 0.8914 (mtm) cc_final: 0.8461 (ttm) outliers start: 59 outliers final: 37 residues processed: 103 average time/residue: 0.2688 time to fit residues: 50.4463 Evaluate side-chains 94 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 51 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 950 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.0570 chunk 110 optimal weight: 0.0870 chunk 165 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 137 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 ASN B 126 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22608 Z= 0.183 Angle : 0.651 10.545 30960 Z= 0.322 Chirality : 0.045 0.430 4008 Planarity : 0.003 0.045 3873 Dihedral : 6.945 58.806 4275 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.65 % Favored : 88.93 % Rotamer: Outliers : 2.46 % Allowed : 10.98 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.64 (0.16), residues: 2892 helix: 2.71 (0.20), residues: 675 sheet: -1.78 (0.21), residues: 549 loop : -2.64 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 973 HIS 0.005 0.001 HIS A 421 PHE 0.020 0.001 PHE B 839 TYR 0.015 0.001 TYR B 226 ARG 0.004 0.000 ARG B 978 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 53 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7715 (p0) REVERT: A 249 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9041 (pp) REVERT: A 316 MET cc_start: 0.8441 (mtp) cc_final: 0.8123 (mtp) REVERT: A 980 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7741 (mtm) REVERT: B 86 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: B 718 MET cc_start: 0.8215 (mtp) cc_final: 0.7892 (mtm) REVERT: B 980 MET cc_start: 0.7609 (mmm) cc_final: 0.7247 (mmm) REVERT: C 169 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7884 (p0) REVERT: C 372 MET cc_start: 0.8526 (ttm) cc_final: 0.8225 (ttm) REVERT: C 388 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8683 (mtp) REVERT: C 718 MET cc_start: 0.8275 (mtp) cc_final: 0.7808 (mtm) outliers start: 57 outliers final: 43 residues processed: 103 average time/residue: 0.2895 time to fit residues: 53.7503 Evaluate side-chains 100 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 51 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 994 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 242 optimal weight: 0.0970 chunk 258 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22608 Z= 0.214 Angle : 0.658 10.652 30960 Z= 0.325 Chirality : 0.045 0.431 4008 Planarity : 0.003 0.044 3873 Dihedral : 6.892 59.778 4275 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.45 % Favored : 88.14 % Rotamer: Outliers : 2.55 % Allowed : 11.11 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.57 (0.16), residues: 2892 helix: 2.77 (0.20), residues: 675 sheet: -1.71 (0.21), residues: 549 loop : -2.61 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 973 HIS 0.005 0.001 HIS A 421 PHE 0.019 0.001 PHE B 839 TYR 0.018 0.001 TYR B 61 ARG 0.001 0.000 ARG A 978 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 53 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9025 (pp) REVERT: A 316 MET cc_start: 0.8468 (mtp) cc_final: 0.8159 (mtp) REVERT: A 980 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7778 (mtm) REVERT: B 86 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: B 354 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7548 (mtm) REVERT: B 718 MET cc_start: 0.8233 (mtp) cc_final: 0.7905 (mtm) REVERT: B 731 MET cc_start: 0.8832 (mtm) cc_final: 0.8624 (ttm) REVERT: B 930 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.6694 (p90) REVERT: C 169 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7949 (p0) REVERT: C 372 MET cc_start: 0.8524 (ttm) cc_final: 0.8211 (ttm) REVERT: C 388 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.8845 (mtp) REVERT: C 718 MET cc_start: 0.8290 (mtp) cc_final: 0.7818 (mtm) outliers start: 59 outliers final: 44 residues processed: 105 average time/residue: 0.2616 time to fit residues: 49.0540 Evaluate side-chains 103 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 52 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 930 PHE Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 930 PHE Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 912 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.0770 chunk 273 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 190 optimal weight: 0.0040 chunk 286 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 chunk 228 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.6152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 GLN A 847 GLN B 847 GLN C 851 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22608 Z= 0.141 Angle : 0.630 10.217 30960 Z= 0.312 Chirality : 0.044 0.418 4008 Planarity : 0.003 0.044 3873 Dihedral : 6.570 57.443 4275 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.99 % Favored : 89.59 % Rotamer: Outliers : 2.25 % Allowed : 11.59 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.48 (0.16), residues: 2892 helix: 2.83 (0.20), residues: 675 sheet: -1.65 (0.22), residues: 549 loop : -2.54 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 973 HIS 0.010 0.001 HIS A 140 PHE 0.020 0.001 PHE B 577 TYR 0.018 0.001 TYR A 226 ARG 0.002 0.000 ARG B 978 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 54 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8998 (pp) REVERT: A 316 MET cc_start: 0.8474 (mtp) cc_final: 0.8216 (mtp) REVERT: A 980 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7739 (mtm) REVERT: B 86 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: B 354 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7523 (mtm) REVERT: B 372 MET cc_start: 0.8286 (ttm) cc_final: 0.7975 (ttm) REVERT: B 718 MET cc_start: 0.8261 (mtp) cc_final: 0.7953 (mtm) REVERT: C 169 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7806 (p0) REVERT: C 254 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8648 (pt) REVERT: C 372 MET cc_start: 0.8642 (ttm) cc_final: 0.8160 (mtm) REVERT: C 388 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8830 (mtp) outliers start: 52 outliers final: 41 residues processed: 98 average time/residue: 0.2685 time to fit residues: 47.9736 Evaluate side-chains 100 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 52 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 597 CYS Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 494 ASN Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 602 CYS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 980 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.0870 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.041995 restraints weight = 117194.791| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.12 r_work: 0.2925 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22608 Z= 0.157 Angle : 0.634 13.350 30960 Z= 0.312 Chirality : 0.044 0.419 4008 Planarity : 0.003 0.043 3873 Dihedral : 6.495 57.593 4275 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.13 % Favored : 89.45 % Rotamer: Outliers : 2.33 % Allowed : 11.67 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.36 (0.16), residues: 2892 helix: 2.92 (0.20), residues: 675 sheet: -1.54 (0.22), residues: 531 loop : -2.48 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 973 HIS 0.005 0.001 HIS A 421 PHE 0.015 0.001 PHE B 839 TYR 0.017 0.001 TYR B 226 ARG 0.001 0.000 ARG B 978 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3086.11 seconds wall clock time: 58 minutes 13.40 seconds (3493.40 seconds total)