Starting phenix.real_space_refine on Tue May 13 11:58:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vcv_43141/05_2025/8vcv_43141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vcv_43141/05_2025/8vcv_43141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vcv_43141/05_2025/8vcv_43141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vcv_43141/05_2025/8vcv_43141.map" model { file = "/net/cci-nas-00/data/ceres_data/8vcv_43141/05_2025/8vcv_43141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vcv_43141/05_2025/8vcv_43141.cif" } resolution = 2.8 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= 0.019 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 87 5.16 5 C 6498 2.51 5 N 1696 2.21 5 O 2185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10466 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 625 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 550 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 110 Planarities with less than four sites: {'UNK:plan-1': 110} Unresolved non-hydrogen planarities: 110 Chain: "a" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "b" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "c" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" 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: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" 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: "b" 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: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.85, per 1000 atoms: 0.75 Number of scatterers: 10466 At special positions: 0 Unit cell: (108.418, 109.136, 96.212, 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 87 16.00 O 2185 8.00 N 1696 7.00 C 6498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.09 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.06 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN X 4 " - " MAN X 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-3 " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " " NAG O 1 " - " FUC O 3 " " NAG S 1 " - " FUC S 3 " " NAG V 1 " - " FUC V 3 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG B 301 " - " ASN B 99 " " NAG C 301 " - " ASN C 99 " " NAG D 1 " - " ASN A 119 " " NAG E 1 " - " ASN A 167 " " NAG F 1 " - " ASN A 89 " " NAG G 1 " - " ASN A 224 " " NAG I 1 " - " ASN A 79 " " NAG J 1 " - " ASN A 109 " " NAG K 1 " - " ASN B 79 " " NAG M 1 " - " ASN B 89 " " NAG N 1 " - " ASN B 109 " " NAG O 1 " - " ASN B 119 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN B 224 " " NAG R 1 " - " ASN C 167 " " NAG S 1 " - " ASN C 119 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 89 " " NAG V 1 " - " ASN C 109 " " NAG W 1 " - " ASN C 224 " " NAG X 1 " - " ASN a 365 " " NAG Y 1 " - " ASN a 395 " " NAG Z 1 " - " ASN b 365 " " NAG a 900 " - " ASN a 373 " " NAG a 901 " - " ASN a 390 " " NAG b 701 " - " ASN b 373 " " NAG b 702 " - " ASN b 395 " " NAG b 703 " - " ASN b 390 " " NAG c 701 " - " ASN c 390 " " NAG d 1 " - " ASN c 365 " " NAG e 1 " - " ASN c 373 " " NAG f 1 " - " ASN c 395 " Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 17 sheets defined 41.4% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.897A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.790A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.636A pdb=" N ARG A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'B' and resid 75 through 81 removed outlier: 4.310A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.819A pdb=" N LYS B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.925A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 203 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.496A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.688A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.858A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'a' and resid 281 through 285 removed outlier: 4.008A pdb=" N LEU a 285 " --> pdb=" O ARG a 282 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.562A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.594A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 413 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.642A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.546A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 413 Processing helix chain 'c' and resid 281 through 285 removed outlier: 3.546A pdb=" N LEU c 285 " --> pdb=" O ARG c 282 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 334 through 345 removed outlier: 6.003A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.653A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 89 removed outlier: 6.860A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 7 removed outlier: 7.728A pdb=" N UNK H 76 " --> pdb=" O UNK H 72 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N UNK H 72 " --> pdb=" O UNK H 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.868A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N UNK H 96 " --> pdb=" O UNK H 100N" (cutoff:3.500A) removed outlier: 7.650A pdb=" N UNK H 100N" --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N UNK H 98 " --> pdb=" O UNK H 100L" (cutoff:3.500A) removed outlier: 9.357A pdb=" N UNK H 100L" --> pdb=" O UNK H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.868A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.385A pdb=" N UNK L 43 " --> pdb=" O UNK L 39 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N UNK L 39 " --> pdb=" O UNK L 43 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK L 45 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N UNK L 86 " --> pdb=" O UNK L 101 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N UNK L 101 " --> pdb=" O UNK L 86 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N UNK L 88 " --> pdb=" O UNK L 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB4, first strand: chain 'a' and resid 388 through 389 removed outlier: 3.583A pdb=" N SER a 392 " --> pdb=" O SER a 389 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB6, first strand: chain 'b' and resid 388 through 389 removed outlier: 3.584A pdb=" N SER b 392 " --> pdb=" O SER b 389 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB8, first strand: chain 'c' and resid 388 through 389 422 hydrogen bonds defined for protein. 1113 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: 3.71 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2176 1.33 - 1.46: 2922 1.46 - 1.58: 5414 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 10644 Sorted by residual: bond pdb=" N ARG b 325 " pdb=" CA ARG b 325 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.28e-02 6.10e+03 8.02e+00 bond pdb=" N THR B 215 " pdb=" CA THR B 215 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.64e+00 bond pdb=" N MET B 214 " pdb=" CA MET B 214 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.21e-02 6.83e+03 7.52e+00 bond pdb=" N CYS A 207 " pdb=" CA CYS A 207 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.33e+00 bond pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.28e+00 ... (remaining 10639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 13579 1.82 - 3.64: 741 3.64 - 5.46: 127 5.46 - 7.28: 16 7.28 - 9.10: 2 Bond angle restraints: 14465 Sorted by residual: angle pdb=" CA CYS C 231 " pdb=" C CYS C 231 " pdb=" O CYS C 231 " ideal model delta sigma weight residual 122.41 117.69 4.72 1.21e+00 6.83e-01 1.52e+01 angle pdb=" CA GLU C 228 " pdb=" C GLU C 228 " pdb=" O GLU C 228 " ideal model delta sigma weight residual 121.45 117.42 4.03 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N PHE C 233 " pdb=" CA PHE C 233 " pdb=" C PHE C 233 " ideal model delta sigma weight residual 113.55 108.96 4.59 1.26e+00 6.30e-01 1.33e+01 angle pdb=" C UNK L 79 " pdb=" N UNK L 80 " pdb=" CA UNK L 80 " ideal model delta sigma weight residual 121.70 128.12 -6.42 1.80e+00 3.09e-01 1.27e+01 angle pdb=" CA THR B 215 " pdb=" C THR B 215 " pdb=" O THR B 215 " ideal model delta sigma weight residual 121.16 117.31 3.85 1.13e+00 7.83e-01 1.16e+01 ... (remaining 14460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 6936 21.64 - 43.27: 257 43.27 - 64.90: 56 64.90 - 86.54: 55 86.54 - 108.17: 32 Dihedral angle restraints: 7336 sinusoidal: 3606 harmonic: 3730 Sorted by residual: dihedral pdb=" CB CYS C 180 " pdb=" SG CYS C 180 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual -86.00 -18.57 -67.43 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS c 360 " pdb=" CB CYS c 360 " ideal model delta sinusoidal sigma weight residual -86.00 -146.21 60.21 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual -86.00 -30.51 -55.49 1 1.00e+01 1.00e-02 4.16e+01 ... (remaining 7333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1751 0.088 - 0.176: 106 0.176 - 0.264: 18 0.264 - 0.352: 2 0.352 - 0.439: 1 Chirality restraints: 1878 Sorted by residual: chirality pdb=" C1 MAN X 4 " pdb=" O3 BMA X 3 " pdb=" C2 MAN X 4 " pdb=" O5 MAN X 4 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.37e+01 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.00e+01 ... (remaining 1875 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.201 2.00e-02 2.50e+03 1.68e-01 3.52e+02 pdb=" C7 NAG Y 1 " 0.050 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.279 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 703 " 0.119 2.00e-02 2.50e+03 9.88e-02 1.22e+02 pdb=" C7 NAG b 703 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG b 703 " 0.088 2.00e-02 2.50e+03 pdb=" N2 NAG b 703 " -0.160 2.00e-02 2.50e+03 pdb=" O7 NAG b 703 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 901 " -0.108 2.00e-02 2.50e+03 8.90e-02 9.90e+01 pdb=" C7 NAG a 901 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG a 901 " -0.081 2.00e-02 2.50e+03 pdb=" N2 NAG a 901 " 0.143 2.00e-02 2.50e+03 pdb=" O7 NAG a 901 " 0.018 2.00e-02 2.50e+03 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 123 2.66 - 3.22: 9624 3.22 - 3.78: 16023 3.78 - 4.34: 22764 4.34 - 4.90: 36632 Nonbonded interactions: 85166 Sorted by model distance: nonbonded pdb=" OG1 THR A 182 " pdb=" OD1 ASN A 185 " model vdw 2.095 3.040 nonbonded pdb=" O ALA C 195 " pdb=" OG SER C 199 " model vdw 2.103 3.040 nonbonded pdb=" OG SER C 246 " pdb=" OD2 ASP c 347 " model vdw 2.108 3.040 nonbonded pdb=" OG1 THR A 81 " pdb=" OD1 ASN a 319 " model vdw 2.219 3.040 nonbonded pdb=" OG SER b 269 " pdb=" O PRO b 275 " model vdw 2.224 3.040 ... (remaining 85161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'e' selection = chain 'f' } ncs_group { reference = (chain 'H' and resid 19 through 111) selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) } ncs_group { reference = (chain 'a' and (resid 260 through 413 or resid 900)) selection = (chain 'b' and (resid 260 through 413 or resid 701)) selection = chain 'c' } 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: 10.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.050 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.006 0.069 10741 Z= 0.298 Angle : 0.994 17.266 14735 Z= 0.484 Chirality : 0.050 0.439 1878 Planarity : 0.008 0.168 1748 Dihedral : 15.781 108.175 4853 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1017 helix: -0.30 (0.26), residues: 357 sheet: -0.17 (0.46), residues: 111 loop : -0.38 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 210 HIS 0.008 0.002 HIS C 92 PHE 0.011 0.002 PHE B 117 TYR 0.014 0.001 TYR C 253 ARG 0.004 0.001 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.02911 ( 33) link_NAG-ASN : angle 3.09168 ( 99) link_ALPHA1-6 : bond 0.00054 ( 1) link_ALPHA1-6 : angle 2.38264 ( 3) link_BETA1-4 : bond 0.00748 ( 32) link_BETA1-4 : angle 2.18418 ( 96) link_ALPHA1-2 : bond 0.00682 ( 2) link_ALPHA1-2 : angle 1.59138 ( 6) link_ALPHA1-3 : bond 0.00950 ( 3) link_ALPHA1-3 : angle 1.43695 ( 9) hydrogen bonds : bond 0.14497 ( 411) hydrogen bonds : angle 6.38612 ( 1113) link_BETA1-6 : bond 0.00457 ( 5) link_BETA1-6 : angle 1.61508 ( 15) SS BOND : bond 0.01581 ( 21) SS BOND : angle 3.97936 ( 42) covalent geometry : bond 0.00562 (10644) covalent geometry : angle 0.92576 (14465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: B 185 ASN cc_start: 0.8510 (m-40) cc_final: 0.8283 (m110) REVERT: C 125 LYS cc_start: 0.8535 (tttp) cc_final: 0.8175 (ttpt) REVERT: a 379 ARG cc_start: 0.7321 (ttp-110) cc_final: 0.7033 (mtm110) REVERT: b 270 GLU cc_start: 0.6524 (mm-30) cc_final: 0.4995 (tm-30) REVERT: b 304 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8192 (mmtm) REVERT: b 379 ARG cc_start: 0.8394 (ttm110) cc_final: 0.7321 (tmm160) REVERT: c 300 LYS cc_start: 0.9035 (mttp) cc_final: 0.8805 (mttt) REVERT: c 401 ASP cc_start: 0.8892 (m-30) cc_final: 0.8634 (m-30) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 1.3935 time to fit residues: 287.8432 Evaluate side-chains 159 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.0060 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN C 185 ASN C 218 GLN a 324 GLN b 331 GLN b 354 HIS c 342 ASN c 354 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122599 restraints weight = 11413.995| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.92 r_work: 0.3233 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10741 Z= 0.153 Angle : 0.680 9.220 14735 Z= 0.315 Chirality : 0.043 0.280 1878 Planarity : 0.004 0.038 1748 Dihedral : 10.803 72.432 2894 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.72 % Allowed : 7.74 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.27), residues: 1017 helix: 0.35 (0.28), residues: 345 sheet: 0.17 (0.43), residues: 144 loop : -0.00 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.010 0.001 PHE B 117 TYR 0.012 0.001 TYR C 253 ARG 0.006 0.001 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 33) link_NAG-ASN : angle 2.28591 ( 99) link_ALPHA1-6 : bond 0.00581 ( 1) link_ALPHA1-6 : angle 1.05609 ( 3) link_BETA1-4 : bond 0.00465 ( 32) link_BETA1-4 : angle 2.30125 ( 96) link_ALPHA1-2 : bond 0.00516 ( 2) link_ALPHA1-2 : angle 1.84391 ( 6) link_ALPHA1-3 : bond 0.01374 ( 3) link_ALPHA1-3 : angle 1.50361 ( 9) hydrogen bonds : bond 0.04093 ( 411) hydrogen bonds : angle 4.93366 ( 1113) link_BETA1-6 : bond 0.00401 ( 5) link_BETA1-6 : angle 1.28481 ( 15) SS BOND : bond 0.00402 ( 21) SS BOND : angle 1.91435 ( 42) covalent geometry : bond 0.00349 (10644) covalent geometry : angle 0.62021 (14465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8020 (mp) REVERT: B 134 MET cc_start: 0.9217 (tpp) cc_final: 0.8474 (tpt) REVERT: C 125 LYS cc_start: 0.8632 (tttp) cc_final: 0.8033 (tptp) REVERT: a 282 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7662 (ttp80) REVERT: a 379 ARG cc_start: 0.7046 (ttp-110) cc_final: 0.6736 (mtm110) REVERT: b 270 GLU cc_start: 0.6095 (mm-30) cc_final: 0.4295 (tm-30) REVERT: b 304 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8017 (mmtm) REVERT: b 321 GLN cc_start: 0.8490 (mm110) cc_final: 0.8207 (mm110) REVERT: b 379 ARG cc_start: 0.8280 (ttm110) cc_final: 0.6597 (tmm160) REVERT: b 384 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8276 (mtmt) outliers start: 16 outliers final: 5 residues processed: 186 average time/residue: 1.3399 time to fit residues: 266.0938 Evaluate side-chains 166 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain c residue 295 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 96 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN C 146 ASN C 218 GLN a 324 GLN b 331 GLN b 354 HIS c 342 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.145579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121230 restraints weight = 11485.248| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.93 r_work: 0.3197 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10741 Z= 0.155 Angle : 0.660 8.744 14735 Z= 0.303 Chirality : 0.042 0.264 1878 Planarity : 0.004 0.050 1748 Dihedral : 8.398 67.564 2894 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.04 % Allowed : 8.60 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1017 helix: 0.46 (0.28), residues: 345 sheet: 0.46 (0.43), residues: 144 loop : -0.01 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 PHE 0.011 0.002 PHE B 117 TYR 0.010 0.001 TYR C 253 ARG 0.008 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 33) link_NAG-ASN : angle 2.31035 ( 99) link_ALPHA1-6 : bond 0.00640 ( 1) link_ALPHA1-6 : angle 1.19686 ( 3) link_BETA1-4 : bond 0.00390 ( 32) link_BETA1-4 : angle 2.22110 ( 96) link_ALPHA1-2 : bond 0.00372 ( 2) link_ALPHA1-2 : angle 1.91296 ( 6) link_ALPHA1-3 : bond 0.01180 ( 3) link_ALPHA1-3 : angle 1.40842 ( 9) hydrogen bonds : bond 0.03797 ( 411) hydrogen bonds : angle 4.73290 ( 1113) link_BETA1-6 : bond 0.00322 ( 5) link_BETA1-6 : angle 1.25916 ( 15) SS BOND : bond 0.00661 ( 21) SS BOND : angle 1.70795 ( 42) covalent geometry : bond 0.00361 (10644) covalent geometry : angle 0.60053 (14465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8004 (mp) REVERT: C 125 LYS cc_start: 0.8641 (tttp) cc_final: 0.8023 (tptp) REVERT: a 379 ARG cc_start: 0.7127 (ttp-110) cc_final: 0.6769 (mtm110) REVERT: b 270 GLU cc_start: 0.6122 (mm-30) cc_final: 0.4211 (tm-30) REVERT: b 273 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8228 (p0) REVERT: b 304 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8003 (mmtm) REVERT: b 321 GLN cc_start: 0.8489 (mm110) cc_final: 0.8192 (mm110) REVERT: b 379 ARG cc_start: 0.8282 (ttm110) cc_final: 0.6551 (tmm160) REVERT: b 384 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8287 (mtmt) REVERT: c 270 GLU cc_start: 0.5838 (tp30) cc_final: 0.5095 (mm-30) REVERT: c 332 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7920 (ttt) outliers start: 19 outliers final: 7 residues processed: 178 average time/residue: 1.2740 time to fit residues: 242.9985 Evaluate side-chains 165 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain c residue 332 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 84 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN C 218 GLN a 324 GLN b 331 GLN b 338 ASN b 354 HIS c 342 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.147334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123127 restraints weight = 11358.815| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.92 r_work: 0.3230 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10741 Z= 0.116 Angle : 0.590 7.772 14735 Z= 0.275 Chirality : 0.039 0.235 1878 Planarity : 0.003 0.044 1748 Dihedral : 6.697 60.746 2894 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.04 % Allowed : 10.43 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1017 helix: 0.68 (0.28), residues: 345 sheet: 0.57 (0.42), residues: 147 loop : 0.03 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.007 0.001 PHE B 117 TYR 0.011 0.001 TYR B 66 ARG 0.009 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 33) link_NAG-ASN : angle 2.15820 ( 99) link_ALPHA1-6 : bond 0.00762 ( 1) link_ALPHA1-6 : angle 1.46526 ( 3) link_BETA1-4 : bond 0.00447 ( 32) link_BETA1-4 : angle 2.04664 ( 96) link_ALPHA1-2 : bond 0.00379 ( 2) link_ALPHA1-2 : angle 1.77894 ( 6) link_ALPHA1-3 : bond 0.01221 ( 3) link_ALPHA1-3 : angle 1.33869 ( 9) hydrogen bonds : bond 0.03200 ( 411) hydrogen bonds : angle 4.48355 ( 1113) link_BETA1-6 : bond 0.00313 ( 5) link_BETA1-6 : angle 1.23035 ( 15) SS BOND : bond 0.00370 ( 21) SS BOND : angle 1.48011 ( 42) covalent geometry : bond 0.00262 (10644) covalent geometry : angle 0.53306 (14465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7931 (mp) REVERT: A 125 LYS cc_start: 0.8563 (ttmt) cc_final: 0.7867 (tptt) REVERT: B 67 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: C 125 LYS cc_start: 0.8636 (tttp) cc_final: 0.8038 (tptp) REVERT: a 379 ARG cc_start: 0.7038 (ttp-110) cc_final: 0.6774 (mtm110) REVERT: b 270 GLU cc_start: 0.6034 (mm-30) cc_final: 0.4138 (tm-30) REVERT: b 304 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8015 (mmtm) REVERT: b 321 GLN cc_start: 0.8452 (mm110) cc_final: 0.8191 (mm110) REVERT: b 379 ARG cc_start: 0.8277 (ttm110) cc_final: 0.6597 (tmm160) REVERT: c 283 TRP cc_start: 0.7728 (m100) cc_final: 0.7383 (m-90) outliers start: 19 outliers final: 8 residues processed: 173 average time/residue: 1.3137 time to fit residues: 244.8735 Evaluate side-chains 165 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN B 218 GLN C 218 GLN a 324 GLN b 331 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117458 restraints weight = 11359.264| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.95 r_work: 0.3157 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10741 Z= 0.226 Angle : 0.724 7.754 14735 Z= 0.332 Chirality : 0.044 0.280 1878 Planarity : 0.004 0.049 1748 Dihedral : 7.151 65.206 2894 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.33 % Allowed : 9.89 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1017 helix: 0.33 (0.28), residues: 345 sheet: 0.62 (0.41), residues: 132 loop : -0.08 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 283 HIS 0.006 0.001 HIS c 398 PHE 0.012 0.002 PHE B 117 TYR 0.014 0.002 TYR B 66 ARG 0.011 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 33) link_NAG-ASN : angle 2.49731 ( 99) link_ALPHA1-6 : bond 0.00763 ( 1) link_ALPHA1-6 : angle 1.04183 ( 3) link_BETA1-4 : bond 0.00363 ( 32) link_BETA1-4 : angle 2.39152 ( 96) link_ALPHA1-2 : bond 0.00240 ( 2) link_ALPHA1-2 : angle 1.92274 ( 6) link_ALPHA1-3 : bond 0.01037 ( 3) link_ALPHA1-3 : angle 1.51178 ( 9) hydrogen bonds : bond 0.04170 ( 411) hydrogen bonds : angle 4.86428 ( 1113) link_BETA1-6 : bond 0.00243 ( 5) link_BETA1-6 : angle 1.27868 ( 15) SS BOND : bond 0.00458 ( 21) SS BOND : angle 1.99713 ( 42) covalent geometry : bond 0.00540 (10644) covalent geometry : angle 0.66150 (14465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8038 (mp) REVERT: A 214 MET cc_start: 0.6634 (mtt) cc_final: 0.6434 (tpt) REVERT: B 67 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: C 60 SER cc_start: 0.5895 (t) cc_final: 0.5681 (m) REVERT: C 82 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.7730 (mtm) REVERT: C 125 LYS cc_start: 0.8695 (tttp) cc_final: 0.8086 (tptp) REVERT: C 251 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8026 (t0) REVERT: a 332 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.6798 (tpt) REVERT: b 304 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8063 (mmtm) REVERT: b 321 GLN cc_start: 0.8525 (mm110) cc_final: 0.8259 (mm110) REVERT: b 379 ARG cc_start: 0.8352 (ttm110) cc_final: 0.6815 (ttp-170) REVERT: b 384 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8376 (mtmt) REVERT: b 412 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7943 (p) REVERT: c 270 GLU cc_start: 0.6162 (tp30) cc_final: 0.5517 (mm-30) outliers start: 31 outliers final: 15 residues processed: 170 average time/residue: 1.3654 time to fit residues: 248.3339 Evaluate side-chains 173 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN a 324 GLN b 331 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119038 restraints weight = 11408.030| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.96 r_work: 0.3180 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10741 Z= 0.164 Angle : 0.648 8.488 14735 Z= 0.299 Chirality : 0.040 0.247 1878 Planarity : 0.004 0.053 1748 Dihedral : 6.639 62.613 2894 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.26 % Allowed : 11.40 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1017 helix: 0.43 (0.28), residues: 345 sheet: 0.66 (0.41), residues: 132 loop : -0.10 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 PHE 0.010 0.002 PHE B 191 TYR 0.014 0.001 TYR B 66 ARG 0.011 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 33) link_NAG-ASN : angle 2.36222 ( 99) link_ALPHA1-6 : bond 0.00750 ( 1) link_ALPHA1-6 : angle 1.21784 ( 3) link_BETA1-4 : bond 0.00398 ( 32) link_BETA1-4 : angle 2.16663 ( 96) link_ALPHA1-2 : bond 0.00256 ( 2) link_ALPHA1-2 : angle 1.80502 ( 6) link_ALPHA1-3 : bond 0.01022 ( 3) link_ALPHA1-3 : angle 1.27230 ( 9) hydrogen bonds : bond 0.03635 ( 411) hydrogen bonds : angle 4.68067 ( 1113) link_BETA1-6 : bond 0.00205 ( 5) link_BETA1-6 : angle 1.28976 ( 15) SS BOND : bond 0.00419 ( 21) SS BOND : angle 1.54931 ( 42) covalent geometry : bond 0.00389 (10644) covalent geometry : angle 0.58913 (14465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8009 (mp) REVERT: C 60 SER cc_start: 0.5947 (t) cc_final: 0.5732 (m) REVERT: C 125 LYS cc_start: 0.8686 (tttp) cc_final: 0.8070 (tptp) REVERT: a 332 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.6748 (tpt) REVERT: b 304 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8034 (mmtm) REVERT: b 321 GLN cc_start: 0.8512 (mm110) cc_final: 0.8244 (mm110) REVERT: b 379 ARG cc_start: 0.8321 (ttm110) cc_final: 0.6773 (tmm160) REVERT: b 412 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7836 (p) REVERT: c 270 GLU cc_start: 0.6040 (tp30) cc_final: 0.4911 (mm-30) outliers start: 21 outliers final: 12 residues processed: 168 average time/residue: 1.3163 time to fit residues: 236.2864 Evaluate side-chains 164 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 116 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN a 324 GLN b 331 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118836 restraints weight = 11492.839| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.97 r_work: 0.3202 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10741 Z= 0.164 Angle : 0.649 8.844 14735 Z= 0.299 Chirality : 0.040 0.246 1878 Planarity : 0.003 0.047 1748 Dihedral : 6.443 63.547 2894 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.33 % Allowed : 11.40 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1017 helix: 0.48 (0.28), residues: 345 sheet: 0.80 (0.41), residues: 132 loop : -0.11 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.010 0.002 PHE B 191 TYR 0.013 0.001 TYR B 66 ARG 0.013 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 33) link_NAG-ASN : angle 2.34963 ( 99) link_ALPHA1-6 : bond 0.00775 ( 1) link_ALPHA1-6 : angle 1.20793 ( 3) link_BETA1-4 : bond 0.00393 ( 32) link_BETA1-4 : angle 2.15694 ( 96) link_ALPHA1-2 : bond 0.00227 ( 2) link_ALPHA1-2 : angle 1.82746 ( 6) link_ALPHA1-3 : bond 0.01018 ( 3) link_ALPHA1-3 : angle 1.30451 ( 9) hydrogen bonds : bond 0.03635 ( 411) hydrogen bonds : angle 4.60763 ( 1113) link_BETA1-6 : bond 0.00229 ( 5) link_BETA1-6 : angle 1.27886 ( 15) SS BOND : bond 0.00435 ( 21) SS BOND : angle 1.61363 ( 42) covalent geometry : bond 0.00388 (10644) covalent geometry : angle 0.58992 (14465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8017 (mp) REVERT: A 192 MET cc_start: 0.7939 (mmp) cc_final: 0.7262 (mmt) REVERT: B 67 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: C 125 LYS cc_start: 0.8693 (tttp) cc_final: 0.8067 (tptp) REVERT: C 251 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8107 (t0) REVERT: a 332 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.6763 (tpt) REVERT: b 304 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8078 (mmtm) REVERT: b 321 GLN cc_start: 0.8516 (mm110) cc_final: 0.8244 (mm110) REVERT: b 379 ARG cc_start: 0.8320 (ttm110) cc_final: 0.6768 (tmm160) REVERT: b 412 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7841 (p) REVERT: c 270 GLU cc_start: 0.6131 (tp30) cc_final: 0.5485 (mm-30) outliers start: 31 outliers final: 19 residues processed: 170 average time/residue: 1.2432 time to fit residues: 226.4678 Evaluate side-chains 170 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 209 ASN B 189 GLN B 218 GLN B 247 GLN a 324 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116061 restraints weight = 11505.819| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.94 r_work: 0.3140 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10741 Z= 0.245 Angle : 0.747 8.183 14735 Z= 0.342 Chirality : 0.044 0.283 1878 Planarity : 0.004 0.062 1748 Dihedral : 7.089 66.161 2894 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.76 % Allowed : 11.51 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1017 helix: 0.23 (0.28), residues: 345 sheet: 0.71 (0.41), residues: 132 loop : -0.21 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 283 HIS 0.008 0.001 HIS A 230 PHE 0.011 0.002 PHE B 233 TYR 0.018 0.002 TYR B 66 ARG 0.012 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 33) link_NAG-ASN : angle 2.59710 ( 99) link_ALPHA1-6 : bond 0.00770 ( 1) link_ALPHA1-6 : angle 1.03912 ( 3) link_BETA1-4 : bond 0.00384 ( 32) link_BETA1-4 : angle 2.42586 ( 96) link_ALPHA1-2 : bond 0.00165 ( 2) link_ALPHA1-2 : angle 1.82981 ( 6) link_ALPHA1-3 : bond 0.00909 ( 3) link_ALPHA1-3 : angle 1.39948 ( 9) hydrogen bonds : bond 0.04247 ( 411) hydrogen bonds : angle 4.86521 ( 1113) link_BETA1-6 : bond 0.00202 ( 5) link_BETA1-6 : angle 1.29969 ( 15) SS BOND : bond 0.00457 ( 21) SS BOND : angle 2.06515 ( 42) covalent geometry : bond 0.00590 (10644) covalent geometry : angle 0.68243 (14465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 67 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: C 82 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7733 (mtm) REVERT: C 125 LYS cc_start: 0.8730 (tttp) cc_final: 0.8104 (tptp) REVERT: C 251 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7995 (t0) REVERT: a 332 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.6867 (tpt) REVERT: b 273 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8224 (p0) REVERT: b 304 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8151 (mmtm) REVERT: b 321 GLN cc_start: 0.8546 (mm110) cc_final: 0.8280 (mm110) REVERT: b 379 ARG cc_start: 0.8358 (ttm110) cc_final: 0.6792 (tmm160) REVERT: b 412 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7885 (p) REVERT: c 270 GLU cc_start: 0.6203 (tp30) cc_final: 0.5621 (mm-30) outliers start: 35 outliers final: 21 residues processed: 166 average time/residue: 1.2871 time to fit residues: 228.9029 Evaluate side-chains 174 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 273 ASP Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 334 ILE Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 302 ASN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN B 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119292 restraints weight = 11481.119| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.95 r_work: 0.3214 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10741 Z= 0.139 Angle : 0.631 10.455 14735 Z= 0.292 Chirality : 0.040 0.228 1878 Planarity : 0.003 0.059 1748 Dihedral : 6.491 63.552 2894 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.37 % Allowed : 13.01 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1017 helix: 0.54 (0.28), residues: 342 sheet: 0.82 (0.42), residues: 132 loop : -0.18 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.008 0.001 PHE c 399 TYR 0.012 0.001 TYR B 66 ARG 0.014 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 33) link_NAG-ASN : angle 2.34406 ( 99) link_ALPHA1-6 : bond 0.00753 ( 1) link_ALPHA1-6 : angle 1.28740 ( 3) link_BETA1-4 : bond 0.00419 ( 32) link_BETA1-4 : angle 2.04327 ( 96) link_ALPHA1-2 : bond 0.00242 ( 2) link_ALPHA1-2 : angle 1.73925 ( 6) link_ALPHA1-3 : bond 0.01024 ( 3) link_ALPHA1-3 : angle 1.22010 ( 9) hydrogen bonds : bond 0.03445 ( 411) hydrogen bonds : angle 4.57555 ( 1113) link_BETA1-6 : bond 0.00208 ( 5) link_BETA1-6 : angle 1.29943 ( 15) SS BOND : bond 0.00366 ( 21) SS BOND : angle 1.46770 ( 42) covalent geometry : bond 0.00326 (10644) covalent geometry : angle 0.57442 (14465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8061 (mp) REVERT: B 67 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: C 125 LYS cc_start: 0.8708 (tttp) cc_final: 0.8063 (tptp) REVERT: a 332 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.6818 (tpt) REVERT: b 291 LYS cc_start: 0.8594 (mttm) cc_final: 0.8312 (mttm) REVERT: b 304 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8090 (mmtm) REVERT: b 321 GLN cc_start: 0.8493 (mm110) cc_final: 0.8222 (mm110) REVERT: b 379 ARG cc_start: 0.8301 (ttm110) cc_final: 0.6777 (tmm160) REVERT: b 412 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7844 (p) REVERT: c 270 GLU cc_start: 0.6098 (tp30) cc_final: 0.5448 (mm-30) outliers start: 22 outliers final: 15 residues processed: 163 average time/residue: 1.3304 time to fit residues: 231.8856 Evaluate side-chains 167 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 70 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN B 218 GLN a 324 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120382 restraints weight = 11372.674| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.92 r_work: 0.3229 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10741 Z= 0.135 Angle : 0.631 13.439 14735 Z= 0.295 Chirality : 0.040 0.325 1878 Planarity : 0.003 0.066 1748 Dihedral : 6.303 63.265 2894 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.37 % Allowed : 13.33 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1017 helix: 0.63 (0.28), residues: 342 sheet: 0.88 (0.41), residues: 132 loop : -0.16 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.007 0.001 PHE b 293 TYR 0.010 0.001 TYR B 66 ARG 0.016 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 33) link_NAG-ASN : angle 2.28758 ( 99) link_ALPHA1-6 : bond 0.00802 ( 1) link_ALPHA1-6 : angle 1.31743 ( 3) link_BETA1-4 : bond 0.00402 ( 32) link_BETA1-4 : angle 1.97750 ( 96) link_ALPHA1-2 : bond 0.00204 ( 2) link_ALPHA1-2 : angle 1.75585 ( 6) link_ALPHA1-3 : bond 0.00996 ( 3) link_ALPHA1-3 : angle 1.22155 ( 9) hydrogen bonds : bond 0.03393 ( 411) hydrogen bonds : angle 4.54076 ( 1113) link_BETA1-6 : bond 0.00236 ( 5) link_BETA1-6 : angle 1.26780 ( 15) SS BOND : bond 0.00528 ( 21) SS BOND : angle 1.93222 ( 42) covalent geometry : bond 0.00320 (10644) covalent geometry : angle 0.57306 (14465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8034 (mp) REVERT: B 192 MET cc_start: 0.8023 (tmt) cc_final: 0.7133 (mtt) REVERT: C 101 THR cc_start: 0.9138 (m) cc_final: 0.8814 (p) REVERT: C 125 LYS cc_start: 0.8712 (tttp) cc_final: 0.8085 (tptp) REVERT: a 332 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.6795 (tpt) REVERT: b 304 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8111 (mmtm) REVERT: b 321 GLN cc_start: 0.8505 (mm110) cc_final: 0.8238 (mm110) REVERT: b 379 ARG cc_start: 0.8329 (ttm110) cc_final: 0.6819 (tmm160) REVERT: c 270 GLU cc_start: 0.6078 (tp30) cc_final: 0.5445 (mm-30) outliers start: 22 outliers final: 13 residues processed: 165 average time/residue: 1.2802 time to fit residues: 226.6228 Evaluate side-chains 166 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 86 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN a 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121158 restraints weight = 11325.520| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.92 r_work: 0.3237 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10741 Z= 0.129 Angle : 0.627 13.279 14735 Z= 0.293 Chirality : 0.039 0.297 1878 Planarity : 0.003 0.065 1748 Dihedral : 6.022 62.077 2894 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.83 % Allowed : 13.87 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1017 helix: 0.69 (0.29), residues: 342 sheet: 0.92 (0.42), residues: 132 loop : -0.14 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.005 0.001 HIS A 230 PHE 0.008 0.001 PHE b 293 TYR 0.013 0.001 TYR B 66 ARG 0.016 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 33) link_NAG-ASN : angle 2.23890 ( 99) link_ALPHA1-6 : bond 0.00839 ( 1) link_ALPHA1-6 : angle 1.35918 ( 3) link_BETA1-4 : bond 0.00413 ( 32) link_BETA1-4 : angle 1.90268 ( 96) link_ALPHA1-2 : bond 0.00211 ( 2) link_ALPHA1-2 : angle 1.73041 ( 6) link_ALPHA1-3 : bond 0.01021 ( 3) link_ALPHA1-3 : angle 1.20297 ( 9) hydrogen bonds : bond 0.03324 ( 411) hydrogen bonds : angle 4.48503 ( 1113) link_BETA1-6 : bond 0.00258 ( 5) link_BETA1-6 : angle 1.26884 ( 15) SS BOND : bond 0.00507 ( 21) SS BOND : angle 1.87191 ( 42) covalent geometry : bond 0.00307 (10644) covalent geometry : angle 0.57207 (14465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7287.08 seconds wall clock time: 126 minutes 59.69 seconds (7619.69 seconds total)