Starting phenix.real_space_refine on Wed Sep 17 18:44:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vcv_43141/09_2025/8vcv_43141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vcv_43141/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vcv_43141/09_2025/8vcv_43141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vcv_43141/09_2025/8vcv_43141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vcv_43141/09_2025/8vcv_43141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vcv_43141/09_2025/8vcv_43141.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.28, per 1000 atoms: 0.31 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: 1.67 Conformation dependent library (CDL) restraints added in 342.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 1.67 Time building geometry restraints manager: 2.02 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 900) selection = (chain 'b' and resid 260 through 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: 10.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.700 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.270 ------------------------------------------------------------------------------- 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 : 3.12 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG A 248 TYR 0.014 0.001 TYR C 253 PHE 0.011 0.002 PHE B 117 TRP 0.016 0.001 TRP A 210 HIS 0.008 0.002 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00562 (10644) covalent geometry : angle 0.92576 (14465) SS BOND : bond 0.01581 ( 21) SS BOND : angle 3.97936 ( 42) hydrogen bonds : bond 0.14497 ( 411) hydrogen bonds : angle 6.38612 ( 1113) 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) 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_BETA1-6 : bond 0.00457 ( 5) link_BETA1-6 : angle 1.61508 ( 15) link_NAG-ASN : bond 0.02911 ( 33) link_NAG-ASN : angle 3.09168 ( 99) *********************** 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 : 0.361 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: 0.6489 time to fit residues: 133.8924 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 : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 0.0980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.147713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123460 restraints weight = 11404.895| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.92 r_work: 0.3233 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10741 Z= 0.157 Angle : 0.679 9.133 14735 Z= 0.315 Chirality : 0.043 0.283 1878 Planarity : 0.004 0.038 1748 Dihedral : 10.900 73.054 2894 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.61 % Allowed : 7.74 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.27), residues: 1017 helix: 0.35 (0.28), residues: 345 sheet: 0.16 (0.43), residues: 144 loop : -0.00 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 282 TYR 0.013 0.001 TYR C 253 PHE 0.011 0.001 PHE B 117 TRP 0.014 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00359 (10644) covalent geometry : angle 0.62071 (14465) SS BOND : bond 0.00388 ( 21) SS BOND : angle 1.78017 ( 42) hydrogen bonds : bond 0.04127 ( 411) hydrogen bonds : angle 4.94761 ( 1113) link_ALPHA1-2 : bond 0.00508 ( 2) link_ALPHA1-2 : angle 1.83038 ( 6) link_ALPHA1-3 : bond 0.01261 ( 3) link_ALPHA1-3 : angle 1.36616 ( 9) link_ALPHA1-6 : bond 0.00599 ( 1) link_ALPHA1-6 : angle 1.11427 ( 3) link_BETA1-4 : bond 0.00444 ( 32) link_BETA1-4 : angle 2.27147 ( 96) link_BETA1-6 : bond 0.00396 ( 5) link_BETA1-6 : angle 1.28920 ( 15) link_NAG-ASN : bond 0.00282 ( 33) link_NAG-ASN : angle 2.31725 ( 99) *********************** 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 191 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 134 MET cc_start: 0.9211 (tpp) cc_final: 0.8469 (tpt) REVERT: C 125 LYS cc_start: 0.8623 (tttp) cc_final: 0.8018 (tptp) REVERT: a 282 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7681 (ttp80) REVERT: a 379 ARG cc_start: 0.7033 (ttp-110) cc_final: 0.6725 (mtm110) REVERT: b 270 GLU cc_start: 0.6087 (mm-30) cc_final: 0.4288 (tm-30) REVERT: b 304 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8024 (mmtm) REVERT: b 321 GLN cc_start: 0.8471 (mm110) cc_final: 0.8135 (mm110) REVERT: b 379 ARG cc_start: 0.8267 (ttm110) cc_final: 0.6584 (tmm160) REVERT: b 384 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8276 (mtmt) outliers start: 15 outliers final: 5 residues processed: 184 average time/residue: 0.6646 time to fit residues: 130.2795 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 : 0.357 ------------------------------------------------------------------------------- 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 21 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3649 r_free = 0.3649 target = 0.146057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121752 restraints weight = 11368.702| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.92 r_work: 0.3204 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10741 Z= 0.151 Angle : 0.657 8.987 14735 Z= 0.301 Chirality : 0.042 0.264 1878 Planarity : 0.004 0.046 1748 Dihedral : 8.652 68.255 2894 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.27), residues: 1017 helix: 0.47 (0.28), residues: 345 sheet: 0.43 (0.43), residues: 144 loop : -0.01 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 282 TYR 0.010 0.001 TYR C 253 PHE 0.011 0.001 PHE B 117 TRP 0.019 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00353 (10644) covalent geometry : angle 0.59767 (14465) SS BOND : bond 0.00417 ( 21) SS BOND : angle 1.68853 ( 42) hydrogen bonds : bond 0.03825 ( 411) hydrogen bonds : angle 4.74930 ( 1113) link_ALPHA1-2 : bond 0.00490 ( 2) link_ALPHA1-2 : angle 1.86884 ( 6) link_ALPHA1-3 : bond 0.01220 ( 3) link_ALPHA1-3 : angle 1.43869 ( 9) link_ALPHA1-6 : bond 0.00651 ( 1) link_ALPHA1-6 : angle 1.20483 ( 3) link_BETA1-4 : bond 0.00396 ( 32) link_BETA1-4 : angle 2.21579 ( 96) link_BETA1-6 : bond 0.00324 ( 5) link_BETA1-6 : angle 1.26934 ( 15) link_NAG-ASN : bond 0.00248 ( 33) link_NAG-ASN : angle 2.30932 ( 99) *********************** 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 189 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8006 (mp) REVERT: C 67 GLU cc_start: 0.8608 (tt0) cc_final: 0.8352 (tt0) REVERT: C 125 LYS cc_start: 0.8633 (tttp) cc_final: 0.8011 (tptp) REVERT: a 379 ARG cc_start: 0.7116 (ttp-110) cc_final: 0.6768 (mtm110) REVERT: b 270 GLU cc_start: 0.6164 (mm-30) cc_final: 0.4244 (tm-30) REVERT: b 273 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8210 (p0) REVERT: b 304 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8000 (mmtm) REVERT: b 321 GLN cc_start: 0.8427 (mm110) cc_final: 0.8136 (mm110) REVERT: b 379 ARG cc_start: 0.8262 (ttm110) cc_final: 0.6545 (tmm160) REVERT: b 384 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8282 (mtmt) REVERT: c 332 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7919 (ttt) outliers start: 19 outliers final: 7 residues processed: 178 average time/residue: 0.6474 time to fit residues: 122.8773 Evaluate side-chains 164 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 290 LEU 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 109 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.142802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118358 restraints weight = 11527.746| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.94 r_work: 0.3166 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10741 Z= 0.190 Angle : 0.692 7.844 14735 Z= 0.319 Chirality : 0.043 0.273 1878 Planarity : 0.004 0.043 1748 Dihedral : 7.255 64.756 2894 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.69 % Allowed : 9.68 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1017 helix: 0.38 (0.28), residues: 345 sheet: 0.55 (0.41), residues: 132 loop : -0.07 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG b 282 TYR 0.012 0.001 TYR B 66 PHE 0.012 0.002 PHE B 117 TRP 0.019 0.001 TRP c 283 HIS 0.007 0.002 HIS c 398 Details of bonding type rmsd covalent geometry : bond 0.00453 (10644) covalent geometry : angle 0.62969 (14465) SS BOND : bond 0.00456 ( 21) SS BOND : angle 1.89000 ( 42) hydrogen bonds : bond 0.03905 ( 411) hydrogen bonds : angle 4.81352 ( 1113) link_ALPHA1-2 : bond 0.00310 ( 2) link_ALPHA1-2 : angle 1.88580 ( 6) link_ALPHA1-3 : bond 0.01119 ( 3) link_ALPHA1-3 : angle 1.46566 ( 9) link_ALPHA1-6 : bond 0.00768 ( 1) link_ALPHA1-6 : angle 1.10519 ( 3) link_BETA1-4 : bond 0.00365 ( 32) link_BETA1-4 : angle 2.34489 ( 96) link_BETA1-6 : bond 0.00262 ( 5) link_BETA1-6 : angle 1.22883 ( 15) link_NAG-ASN : bond 0.00310 ( 33) link_NAG-ASN : angle 2.41545 ( 99) *********************** 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 183 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8043 (mp) REVERT: C 67 GLU cc_start: 0.8585 (tt0) cc_final: 0.8372 (tt0) REVERT: C 82 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7692 (mtm) REVERT: C 95 ILE cc_start: 0.8757 (mt) cc_final: 0.8463 (tt) REVERT: C 125 LYS cc_start: 0.8673 (tttp) cc_final: 0.8057 (tptp) REVERT: a 332 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.6896 (tpt) REVERT: b 270 GLU cc_start: 0.6109 (mm-30) cc_final: 0.4105 (tm-30) REVERT: b 273 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8207 (p0) REVERT: b 304 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8056 (mmtm) REVERT: b 321 GLN cc_start: 0.8476 (mm110) cc_final: 0.8207 (mm110) REVERT: b 379 ARG cc_start: 0.8292 (ttm110) cc_final: 0.6549 (tmm160) REVERT: b 384 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8331 (mtmt) REVERT: c 270 GLU cc_start: 0.6067 (tp30) cc_final: 0.5352 (mm-30) outliers start: 25 outliers final: 9 residues processed: 166 average time/residue: 0.6678 time to fit residues: 118.2986 Evaluate side-chains 163 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain C residue 121 SER 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 273 ASP Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain c residue 295 ASN 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 19 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 b 354 HIS c 342 ASN c 354 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119760 restraints weight = 11417.313| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.95 r_work: 0.3191 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2038 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= 0.159 Angle : 0.648 8.341 14735 Z= 0.299 Chirality : 0.041 0.252 1878 Planarity : 0.004 0.050 1748 Dihedral : 6.818 62.836 2894 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.58 % Allowed : 10.75 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.26), residues: 1017 helix: 0.45 (0.28), residues: 345 sheet: 0.62 (0.41), residues: 132 loop : -0.14 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 282 TYR 0.013 0.001 TYR B 66 PHE 0.008 0.002 PHE A 191 TRP 0.016 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00374 (10644) covalent geometry : angle 0.58743 (14465) SS BOND : bond 0.00423 ( 21) SS BOND : angle 1.71149 ( 42) hydrogen bonds : bond 0.03630 ( 411) hydrogen bonds : angle 4.68831 ( 1113) link_ALPHA1-2 : bond 0.00312 ( 2) link_ALPHA1-2 : angle 1.82127 ( 6) link_ALPHA1-3 : bond 0.01093 ( 3) link_ALPHA1-3 : angle 1.32728 ( 9) link_ALPHA1-6 : bond 0.00752 ( 1) link_ALPHA1-6 : angle 1.23226 ( 3) link_BETA1-4 : bond 0.00393 ( 32) link_BETA1-4 : angle 2.17209 ( 96) link_BETA1-6 : bond 0.00230 ( 5) link_BETA1-6 : angle 1.27118 ( 15) link_NAG-ASN : bond 0.00252 ( 33) link_NAG-ASN : angle 2.35516 ( 99) *********************** 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 181 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8027 (mp) REVERT: C 60 SER cc_start: 0.5971 (t) cc_final: 0.5728 (m) REVERT: C 125 LYS cc_start: 0.8677 (tttp) cc_final: 0.8078 (tptp) REVERT: C 251 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8119 (t0) REVERT: a 332 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.6839 (tpt) REVERT: b 270 GLU cc_start: 0.6048 (mm-30) cc_final: 0.5722 (mm-30) REVERT: b 273 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8210 (p0) REVERT: b 304 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8050 (mmtm) REVERT: b 321 GLN cc_start: 0.8494 (mm110) cc_final: 0.8238 (mm110) REVERT: b 379 ARG cc_start: 0.8332 (ttm110) cc_final: 0.6710 (tmm160) REVERT: b 412 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7955 (p) REVERT: c 270 GLU cc_start: 0.6087 (tp30) cc_final: 0.5345 (mm-30) outliers start: 24 outliers final: 12 residues processed: 169 average time/residue: 0.6797 time to fit residues: 122.5765 Evaluate side-chains 166 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 231 CYS 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 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 341 VAL Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 110 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 120 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 76 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 b 354 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117830 restraints weight = 11474.941| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.94 r_work: 0.3164 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10741 Z= 0.198 Angle : 0.697 8.105 14735 Z= 0.320 Chirality : 0.042 0.264 1878 Planarity : 0.004 0.056 1748 Dihedral : 6.774 63.675 2894 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.80 % Allowed : 11.08 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.26), residues: 1017 helix: 0.34 (0.28), residues: 345 sheet: 0.63 (0.41), residues: 132 loop : -0.16 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG b 282 TYR 0.017 0.001 TYR B 66 PHE 0.011 0.002 PHE B 191 TRP 0.017 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00472 (10644) covalent geometry : angle 0.63585 (14465) SS BOND : bond 0.00465 ( 21) SS BOND : angle 1.80805 ( 42) hydrogen bonds : bond 0.03920 ( 411) hydrogen bonds : angle 4.78142 ( 1113) link_ALPHA1-2 : bond 0.00233 ( 2) link_ALPHA1-2 : angle 1.86211 ( 6) link_ALPHA1-3 : bond 0.00956 ( 3) link_ALPHA1-3 : angle 1.39013 ( 9) link_ALPHA1-6 : bond 0.00766 ( 1) link_ALPHA1-6 : angle 1.11443 ( 3) link_BETA1-4 : bond 0.00371 ( 32) link_BETA1-4 : angle 2.31449 ( 96) link_BETA1-6 : bond 0.00217 ( 5) link_BETA1-6 : angle 1.30526 ( 15) link_NAG-ASN : bond 0.00335 ( 33) link_NAG-ASN : angle 2.46067 ( 99) *********************** 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 181 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8089 (mp) REVERT: C 82 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7717 (mtm) REVERT: C 125 LYS cc_start: 0.8703 (tttp) cc_final: 0.8084 (tptp) REVERT: C 251 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8131 (t0) REVERT: a 332 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.6841 (tpt) REVERT: b 273 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8230 (p0) REVERT: b 304 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8123 (mmtm) REVERT: b 321 GLN cc_start: 0.8508 (mm110) cc_final: 0.8243 (mm110) REVERT: b 379 ARG cc_start: 0.8347 (ttm110) cc_final: 0.6793 (tmm160) REVERT: b 384 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8351 (mtmt) REVERT: b 412 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7875 (p) REVERT: c 270 GLU cc_start: 0.6163 (tp30) cc_final: 0.5512 (mm-30) outliers start: 26 outliers final: 16 residues processed: 168 average time/residue: 0.6411 time to fit residues: 115.2132 Evaluate side-chains 168 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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 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 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 341 VAL Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 b 331 GLN b 354 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118262 restraints weight = 11394.241| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.94 r_work: 0.3199 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2255 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= 0.180 Angle : 0.669 7.774 14735 Z= 0.308 Chirality : 0.041 0.253 1878 Planarity : 0.004 0.055 1748 Dihedral : 6.682 62.864 2894 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.55 % Allowed : 10.86 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1017 helix: 0.44 (0.28), residues: 342 sheet: 0.68 (0.42), residues: 132 loop : -0.16 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG b 282 TYR 0.015 0.001 TYR B 66 PHE 0.009 0.002 PHE B 191 TRP 0.014 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00429 (10644) covalent geometry : angle 0.60861 (14465) SS BOND : bond 0.00391 ( 21) SS BOND : angle 1.70196 ( 42) hydrogen bonds : bond 0.03741 ( 411) hydrogen bonds : angle 4.72212 ( 1113) link_ALPHA1-2 : bond 0.00225 ( 2) link_ALPHA1-2 : angle 1.81514 ( 6) link_ALPHA1-3 : bond 0.00978 ( 3) link_ALPHA1-3 : angle 1.29264 ( 9) link_ALPHA1-6 : bond 0.00766 ( 1) link_ALPHA1-6 : angle 1.16348 ( 3) link_BETA1-4 : bond 0.00385 ( 32) link_BETA1-4 : angle 2.21204 ( 96) link_BETA1-6 : bond 0.00210 ( 5) link_BETA1-6 : angle 1.30470 ( 15) link_NAG-ASN : bond 0.00285 ( 33) link_NAG-ASN : angle 2.42214 ( 99) *********************** 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 188 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 125 LYS cc_start: 0.8698 (tttp) cc_final: 0.8073 (tptp) REVERT: C 251 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8112 (t0) REVERT: a 332 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.6848 (tpt) REVERT: b 304 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8122 (mmtm) REVERT: b 321 GLN cc_start: 0.8485 (mm110) cc_final: 0.8227 (mm110) REVERT: b 379 ARG cc_start: 0.8337 (ttm110) cc_final: 0.6788 (tmm160) REVERT: b 412 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7859 (p) REVERT: c 270 GLU cc_start: 0.6194 (tp30) cc_final: 0.5536 (mm-30) outliers start: 33 outliers final: 19 residues processed: 172 average time/residue: 0.6372 time to fit residues: 117.4059 Evaluate side-chains 172 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 95 ILE Chi-restraints excluded: chain B residue 213 ILE 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 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 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 302 ASN Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 102 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 247 GLN a 324 GLN b 331 GLN b 354 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117433 restraints weight = 11409.365| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.93 r_work: 0.3190 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10741 Z= 0.203 Angle : 0.701 10.047 14735 Z= 0.322 Chirality : 0.042 0.260 1878 Planarity : 0.004 0.062 1748 Dihedral : 6.792 63.332 2894 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.55 % Allowed : 11.29 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.26), residues: 1017 helix: 0.39 (0.28), residues: 342 sheet: 0.70 (0.42), residues: 132 loop : -0.19 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG b 282 TYR 0.015 0.002 TYR B 66 PHE 0.010 0.002 PHE B 191 TRP 0.014 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00488 (10644) covalent geometry : angle 0.63825 (14465) SS BOND : bond 0.00457 ( 21) SS BOND : angle 2.09906 ( 42) hydrogen bonds : bond 0.03909 ( 411) hydrogen bonds : angle 4.75151 ( 1113) link_ALPHA1-2 : bond 0.00221 ( 2) link_ALPHA1-2 : angle 1.81953 ( 6) link_ALPHA1-3 : bond 0.00990 ( 3) link_ALPHA1-3 : angle 1.34450 ( 9) link_ALPHA1-6 : bond 0.00781 ( 1) link_ALPHA1-6 : angle 1.10116 ( 3) link_BETA1-4 : bond 0.00374 ( 32) link_BETA1-4 : angle 2.26652 ( 96) link_BETA1-6 : bond 0.00204 ( 5) link_BETA1-6 : angle 1.29587 ( 15) link_NAG-ASN : bond 0.00323 ( 33) link_NAG-ASN : angle 2.46778 ( 99) *********************** 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 180 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8128 (mp) REVERT: C 82 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7708 (mtm) REVERT: C 125 LYS cc_start: 0.8714 (tttp) cc_final: 0.8086 (tptp) REVERT: C 251 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8106 (t0) REVERT: a 332 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.6865 (tpt) REVERT: b 304 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8119 (mmtm) REVERT: b 321 GLN cc_start: 0.8502 (mm110) cc_final: 0.8236 (mm110) REVERT: b 379 ARG cc_start: 0.8346 (ttm110) cc_final: 0.6798 (tmm160) REVERT: b 412 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7873 (p) REVERT: c 270 GLU cc_start: 0.6178 (tp30) cc_final: 0.5493 (mm-30) outliers start: 33 outliers final: 20 residues processed: 166 average time/residue: 0.6562 time to fit residues: 116.2541 Evaluate side-chains 168 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 213 ILE 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 53 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 b 331 GLN b 354 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118811 restraints weight = 11387.680| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.94 r_work: 0.3176 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2361 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= 0.159 Angle : 0.654 10.199 14735 Z= 0.302 Chirality : 0.040 0.237 1878 Planarity : 0.004 0.062 1748 Dihedral : 6.574 62.511 2894 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.80 % Allowed : 11.83 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.26), residues: 1017 helix: 0.49 (0.28), residues: 342 sheet: 0.72 (0.42), residues: 132 loop : -0.19 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG b 282 TYR 0.013 0.001 TYR B 66 PHE 0.008 0.001 PHE c 399 TRP 0.013 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00378 (10644) covalent geometry : angle 0.59626 (14465) SS BOND : bond 0.00501 ( 21) SS BOND : angle 1.66575 ( 42) hydrogen bonds : bond 0.03608 ( 411) hydrogen bonds : angle 4.62717 ( 1113) link_ALPHA1-2 : bond 0.00220 ( 2) link_ALPHA1-2 : angle 1.76955 ( 6) link_ALPHA1-3 : bond 0.01002 ( 3) link_ALPHA1-3 : angle 1.24377 ( 9) link_ALPHA1-6 : bond 0.00767 ( 1) link_ALPHA1-6 : angle 1.22309 ( 3) link_BETA1-4 : bond 0.00396 ( 32) link_BETA1-4 : angle 2.10210 ( 96) link_BETA1-6 : bond 0.00217 ( 5) link_BETA1-6 : angle 1.29109 ( 15) link_NAG-ASN : bond 0.00245 ( 33) link_NAG-ASN : angle 2.37469 ( 99) *********************** 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 177 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8139 (mp) REVERT: B 192 MET cc_start: 0.7493 (mtt) cc_final: 0.7258 (tmt) REVERT: C 125 LYS cc_start: 0.8706 (tttp) cc_final: 0.8081 (tptp) REVERT: a 332 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.6871 (tpt) REVERT: b 291 LYS cc_start: 0.8624 (mttm) cc_final: 0.8364 (mttm) REVERT: b 304 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8097 (mmtm) REVERT: b 321 GLN cc_start: 0.8488 (mm110) cc_final: 0.8221 (mm110) REVERT: b 379 ARG cc_start: 0.8328 (ttm110) cc_final: 0.6786 (tmm160) REVERT: b 412 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7849 (p) REVERT: c 270 GLU cc_start: 0.6144 (tp30) cc_final: 0.5467 (mm-30) outliers start: 26 outliers final: 17 residues processed: 166 average time/residue: 0.6396 time to fit residues: 113.2939 Evaluate side-chains 169 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 213 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER 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 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 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 a 324 GLN b 331 GLN b 354 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117570 restraints weight = 11369.884| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.92 r_work: 0.3192 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 10741 Z= 0.209 Angle : 0.723 13.205 14735 Z= 0.334 Chirality : 0.043 0.346 1878 Planarity : 0.004 0.068 1748 Dihedral : 6.793 63.352 2894 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.80 % Allowed : 11.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.26), residues: 1017 helix: 0.37 (0.28), residues: 342 sheet: 0.69 (0.42), residues: 132 loop : -0.22 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG b 282 TYR 0.014 0.002 TYR B 66 PHE 0.009 0.002 PHE B 191 TRP 0.014 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00508 (10644) covalent geometry : angle 0.66012 (14465) SS BOND : bond 0.00696 ( 21) SS BOND : angle 2.45042 ( 42) hydrogen bonds : bond 0.03922 ( 411) hydrogen bonds : angle 4.75748 ( 1113) link_ALPHA1-2 : bond 0.00183 ( 2) link_ALPHA1-2 : angle 1.78010 ( 6) link_ALPHA1-3 : bond 0.00924 ( 3) link_ALPHA1-3 : angle 1.31242 ( 9) link_ALPHA1-6 : bond 0.00777 ( 1) link_ALPHA1-6 : angle 1.12488 ( 3) link_BETA1-4 : bond 0.00373 ( 32) link_BETA1-4 : angle 2.22956 ( 96) link_BETA1-6 : bond 0.00188 ( 5) link_BETA1-6 : angle 1.29448 ( 15) link_NAG-ASN : bond 0.00328 ( 33) link_NAG-ASN : angle 2.47217 ( 99) ********************** 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 177 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 179 HIS cc_start: 0.6425 (m90) cc_final: 0.5990 (t70) REVERT: C 82 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7666 (mtm) REVERT: C 125 LYS cc_start: 0.8729 (tttp) cc_final: 0.8100 (tptp) REVERT: C 251 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8077 (t0) REVERT: a 332 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.6893 (tpt) REVERT: b 304 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8112 (mmtm) REVERT: b 321 GLN cc_start: 0.8501 (mm110) cc_final: 0.8233 (mm110) REVERT: b 379 ARG cc_start: 0.8342 (ttm110) cc_final: 0.6800 (tmm160) REVERT: b 412 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7872 (p) REVERT: c 270 GLU cc_start: 0.6185 (tp30) cc_final: 0.5505 (mm-30) outliers start: 26 outliers final: 18 residues processed: 166 average time/residue: 0.6042 time to fit residues: 107.2754 Evaluate side-chains 170 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 213 ILE 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 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 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 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN b 331 GLN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120309 restraints weight = 11433.181| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.95 r_work: 0.3195 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10741 Z= 0.135 Angle : 0.642 13.476 14735 Z= 0.300 Chirality : 0.040 0.300 1878 Planarity : 0.003 0.064 1748 Dihedral : 6.258 61.850 2894 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.26 % Allowed : 12.69 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.26), residues: 1017 helix: 0.29 (0.28), residues: 360 sheet: 0.78 (0.42), residues: 132 loop : -0.20 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG b 282 TYR 0.011 0.001 TYR B 66 PHE 0.008 0.001 PHE c 399 TRP 0.013 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00321 (10644) covalent geometry : angle 0.58643 (14465) SS BOND : bond 0.00582 ( 21) SS BOND : angle 1.94757 ( 42) hydrogen bonds : bond 0.03383 ( 411) hydrogen bonds : angle 4.57564 ( 1113) link_ALPHA1-2 : bond 0.00220 ( 2) link_ALPHA1-2 : angle 1.72970 ( 6) link_ALPHA1-3 : bond 0.01060 ( 3) link_ALPHA1-3 : angle 1.20509 ( 9) link_ALPHA1-6 : bond 0.00799 ( 1) link_ALPHA1-6 : angle 1.33812 ( 3) link_BETA1-4 : bond 0.00420 ( 32) link_BETA1-4 : angle 1.94603 ( 96) link_BETA1-6 : bond 0.00235 ( 5) link_BETA1-6 : angle 1.28101 ( 15) link_NAG-ASN : bond 0.00199 ( 33) link_NAG-ASN : angle 2.29409 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3956.03 seconds wall clock time: 68 minutes 22.03 seconds (4102.03 seconds total)