Starting phenix.real_space_refine on Mon Jul 28 16:30:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vcv_43141/07_2025/8vcv_43141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vcv_43141/07_2025/8vcv_43141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vcv_43141/07_2025/8vcv_43141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vcv_43141/07_2025/8vcv_43141.map" model { file = "/net/cci-nas-00/data/ceres_data/8vcv_43141/07_2025/8vcv_43141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vcv_43141/07_2025/8vcv_43141.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 6498 2.51 5 N 1696 2.21 5 O 2185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10466 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 625 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 550 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 110 Planarities with less than four sites: {'UNK:plan-1': 110} Unresolved non-hydrogen planarities: 110 Chain: "a" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "b" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "c" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.94, per 1000 atoms: 0.85 Number of scatterers: 10466 At special positions: 0 Unit cell: (108.418, 109.136, 96.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2185 8.00 N 1696 7.00 C 6498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.09 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.06 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN X 4 " - " MAN X 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-3 " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " " NAG O 1 " - " FUC O 3 " " NAG S 1 " - " FUC S 3 " " NAG V 1 " - " FUC V 3 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG B 301 " - " ASN B 99 " " NAG C 301 " - " ASN C 99 " " NAG D 1 " - " ASN A 119 " " NAG E 1 " - " ASN A 167 " " NAG F 1 " - " ASN A 89 " " NAG G 1 " - " ASN A 224 " " NAG I 1 " - " ASN A 79 " " NAG J 1 " - " ASN A 109 " " NAG K 1 " - " ASN B 79 " " NAG M 1 " - " ASN B 89 " " NAG N 1 " - " ASN B 109 " " NAG O 1 " - " ASN B 119 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN B 224 " " NAG R 1 " - " ASN C 167 " " NAG S 1 " - " ASN C 119 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 89 " " NAG V 1 " - " ASN C 109 " " NAG W 1 " - " ASN C 224 " " NAG X 1 " - " ASN a 365 " " NAG Y 1 " - " ASN a 395 " " NAG Z 1 " - " ASN b 365 " " NAG a 900 " - " ASN a 373 " " NAG a 901 " - " ASN a 390 " " NAG b 701 " - " ASN b 373 " " NAG b 702 " - " ASN b 395 " " NAG b 703 " - " ASN b 390 " " NAG c 701 " - " ASN c 390 " " NAG d 1 " - " ASN c 365 " " NAG e 1 " - " ASN c 373 " " NAG f 1 " - " ASN c 395 " Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 17 sheets defined 41.4% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.897A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.790A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.636A pdb=" N ARG A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'B' and resid 75 through 81 removed outlier: 4.310A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.819A pdb=" N LYS B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.925A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 203 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.496A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.688A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.858A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'a' and resid 281 through 285 removed outlier: 4.008A pdb=" N LEU a 285 " --> pdb=" O ARG a 282 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.562A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.594A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 413 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.642A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.546A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 413 Processing helix chain 'c' and resid 281 through 285 removed outlier: 3.546A pdb=" N LEU c 285 " --> pdb=" O ARG c 282 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 334 through 345 removed outlier: 6.003A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.653A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 89 removed outlier: 6.860A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 7 removed outlier: 7.728A pdb=" N UNK H 76 " --> pdb=" O UNK H 72 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N UNK H 72 " --> pdb=" O UNK H 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.868A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N UNK H 96 " --> pdb=" O UNK H 100N" (cutoff:3.500A) removed outlier: 7.650A pdb=" N UNK H 100N" --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N UNK H 98 " --> pdb=" O UNK H 100L" (cutoff:3.500A) removed outlier: 9.357A pdb=" N UNK H 100L" --> pdb=" O UNK H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.868A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.385A pdb=" N UNK L 43 " --> pdb=" O UNK L 39 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N UNK L 39 " --> pdb=" O UNK L 43 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK L 45 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N UNK L 86 " --> pdb=" O UNK L 101 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N UNK L 101 " --> pdb=" O UNK L 86 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N UNK L 88 " --> pdb=" O UNK L 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB4, first strand: chain 'a' and resid 388 through 389 removed outlier: 3.583A pdb=" N SER a 392 " --> pdb=" O SER a 389 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB6, first strand: chain 'b' and resid 388 through 389 removed outlier: 3.584A pdb=" N SER b 392 " --> pdb=" O SER b 389 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB8, first strand: chain 'c' and resid 388 through 389 422 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2176 1.33 - 1.46: 2922 1.46 - 1.58: 5414 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 10644 Sorted by residual: bond pdb=" N ARG b 325 " pdb=" CA ARG b 325 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.28e-02 6.10e+03 8.02e+00 bond pdb=" N THR B 215 " pdb=" CA THR B 215 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.64e+00 bond pdb=" N MET B 214 " pdb=" CA MET B 214 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.21e-02 6.83e+03 7.52e+00 bond pdb=" N CYS A 207 " pdb=" CA CYS A 207 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.33e+00 bond pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.28e+00 ... (remaining 10639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 13579 1.82 - 3.64: 741 3.64 - 5.46: 127 5.46 - 7.28: 16 7.28 - 9.10: 2 Bond angle restraints: 14465 Sorted by residual: angle pdb=" CA CYS C 231 " pdb=" C CYS C 231 " pdb=" O CYS C 231 " ideal model delta sigma weight residual 122.41 117.69 4.72 1.21e+00 6.83e-01 1.52e+01 angle pdb=" CA GLU C 228 " pdb=" C GLU C 228 " pdb=" O GLU C 228 " ideal model delta sigma weight residual 121.45 117.42 4.03 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N PHE C 233 " pdb=" CA PHE C 233 " pdb=" C PHE C 233 " ideal model delta sigma weight residual 113.55 108.96 4.59 1.26e+00 6.30e-01 1.33e+01 angle pdb=" C UNK L 79 " pdb=" N UNK L 80 " pdb=" CA UNK L 80 " ideal model delta sigma weight residual 121.70 128.12 -6.42 1.80e+00 3.09e-01 1.27e+01 angle pdb=" CA THR B 215 " pdb=" C THR B 215 " pdb=" O THR B 215 " ideal model delta sigma weight residual 121.16 117.31 3.85 1.13e+00 7.83e-01 1.16e+01 ... (remaining 14460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 6936 21.64 - 43.27: 257 43.27 - 64.90: 56 64.90 - 86.54: 55 86.54 - 108.17: 32 Dihedral angle restraints: 7336 sinusoidal: 3606 harmonic: 3730 Sorted by residual: dihedral pdb=" CB CYS C 180 " pdb=" SG CYS C 180 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual -86.00 -18.57 -67.43 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS c 360 " pdb=" CB CYS c 360 " ideal model delta sinusoidal sigma weight residual -86.00 -146.21 60.21 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual -86.00 -30.51 -55.49 1 1.00e+01 1.00e-02 4.16e+01 ... (remaining 7333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1751 0.088 - 0.176: 106 0.176 - 0.264: 18 0.264 - 0.352: 2 0.352 - 0.439: 1 Chirality restraints: 1878 Sorted by residual: chirality pdb=" C1 MAN X 4 " pdb=" O3 BMA X 3 " pdb=" C2 MAN X 4 " pdb=" O5 MAN X 4 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.37e+01 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.00e+01 ... (remaining 1875 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.201 2.00e-02 2.50e+03 1.68e-01 3.52e+02 pdb=" C7 NAG Y 1 " 0.050 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.279 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 703 " 0.119 2.00e-02 2.50e+03 9.88e-02 1.22e+02 pdb=" C7 NAG b 703 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG b 703 " 0.088 2.00e-02 2.50e+03 pdb=" N2 NAG b 703 " -0.160 2.00e-02 2.50e+03 pdb=" O7 NAG b 703 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 901 " -0.108 2.00e-02 2.50e+03 8.90e-02 9.90e+01 pdb=" C7 NAG a 901 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG a 901 " -0.081 2.00e-02 2.50e+03 pdb=" N2 NAG a 901 " 0.143 2.00e-02 2.50e+03 pdb=" O7 NAG a 901 " 0.018 2.00e-02 2.50e+03 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 123 2.66 - 3.22: 9624 3.22 - 3.78: 16023 3.78 - 4.34: 22764 4.34 - 4.90: 36632 Nonbonded interactions: 85166 Sorted by model distance: nonbonded pdb=" OG1 THR A 182 " pdb=" OD1 ASN A 185 " model vdw 2.095 3.040 nonbonded pdb=" O ALA C 195 " pdb=" OG SER C 199 " model vdw 2.103 3.040 nonbonded pdb=" OG SER C 246 " pdb=" OD2 ASP c 347 " model vdw 2.108 3.040 nonbonded pdb=" OG1 THR A 81 " pdb=" OD1 ASN a 319 " model vdw 2.219 3.040 nonbonded pdb=" OG SER b 269 " pdb=" O PRO b 275 " model vdw 2.224 3.040 ... (remaining 85161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'e' selection = chain 'f' } ncs_group { reference = (chain 'H' and resid 19 through 111) selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) } ncs_group { reference = (chain 'a' and (resid 260 through 413 or resid 900)) selection = (chain 'b' and (resid 260 through 413 or resid 701)) selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.680 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10741 Z= 0.298 Angle : 0.994 17.266 14735 Z= 0.484 Chirality : 0.050 0.439 1878 Planarity : 0.008 0.168 1748 Dihedral : 15.781 108.175 4853 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1017 helix: -0.30 (0.26), residues: 357 sheet: -0.17 (0.46), residues: 111 loop : -0.38 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 210 HIS 0.008 0.002 HIS C 92 PHE 0.011 0.002 PHE B 117 TYR 0.014 0.001 TYR C 253 ARG 0.004 0.001 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.02911 ( 33) link_NAG-ASN : angle 3.09168 ( 99) link_ALPHA1-6 : bond 0.00054 ( 1) link_ALPHA1-6 : angle 2.38264 ( 3) link_BETA1-4 : bond 0.00748 ( 32) link_BETA1-4 : angle 2.18418 ( 96) link_ALPHA1-2 : bond 0.00682 ( 2) link_ALPHA1-2 : angle 1.59138 ( 6) link_ALPHA1-3 : bond 0.00950 ( 3) link_ALPHA1-3 : angle 1.43695 ( 9) hydrogen bonds : bond 0.14497 ( 411) hydrogen bonds : angle 6.38612 ( 1113) link_BETA1-6 : bond 0.00457 ( 5) link_BETA1-6 : angle 1.61508 ( 15) SS BOND : bond 0.01581 ( 21) SS BOND : angle 3.97936 ( 42) covalent geometry : bond 0.00562 (10644) covalent geometry : angle 0.92576 (14465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: B 185 ASN cc_start: 0.8510 (m-40) cc_final: 0.8283 (m110) REVERT: C 125 LYS cc_start: 0.8535 (tttp) cc_final: 0.8175 (ttpt) REVERT: a 379 ARG cc_start: 0.7321 (ttp-110) cc_final: 0.7033 (mtm110) REVERT: b 270 GLU cc_start: 0.6524 (mm-30) cc_final: 0.4995 (tm-30) REVERT: b 304 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8192 (mmtm) REVERT: b 379 ARG cc_start: 0.8394 (ttm110) cc_final: 0.7321 (tmm160) REVERT: c 300 LYS cc_start: 0.9035 (mttp) cc_final: 0.8805 (mttt) REVERT: c 401 ASP cc_start: 0.8892 (m-30) cc_final: 0.8634 (m-30) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 1.4369 time to fit residues: 296.9848 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 : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.0060 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN C 185 ASN C 218 GLN a 324 GLN b 331 GLN b 354 HIS c 342 ASN c 354 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122636 restraints weight = 11413.301| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.92 r_work: 0.3233 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10741 Z= 0.153 Angle : 0.680 9.220 14735 Z= 0.315 Chirality : 0.043 0.280 1878 Planarity : 0.004 0.038 1748 Dihedral : 10.803 72.431 2894 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.72 % Allowed : 7.74 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.27), residues: 1017 helix: 0.35 (0.28), residues: 345 sheet: 0.17 (0.43), residues: 144 loop : -0.00 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.010 0.001 PHE B 117 TYR 0.012 0.001 TYR C 253 ARG 0.006 0.001 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 33) link_NAG-ASN : angle 2.28591 ( 99) link_ALPHA1-6 : bond 0.00581 ( 1) link_ALPHA1-6 : angle 1.05609 ( 3) link_BETA1-4 : bond 0.00465 ( 32) link_BETA1-4 : angle 2.30125 ( 96) link_ALPHA1-2 : bond 0.00516 ( 2) link_ALPHA1-2 : angle 1.84392 ( 6) link_ALPHA1-3 : bond 0.01374 ( 3) link_ALPHA1-3 : angle 1.50361 ( 9) hydrogen bonds : bond 0.04093 ( 411) hydrogen bonds : angle 4.93366 ( 1113) link_BETA1-6 : bond 0.00401 ( 5) link_BETA1-6 : angle 1.28481 ( 15) SS BOND : bond 0.00402 ( 21) SS BOND : angle 1.91435 ( 42) covalent geometry : bond 0.00349 (10644) covalent geometry : angle 0.62021 (14465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 134 MET cc_start: 0.9217 (tpp) cc_final: 0.8473 (tpt) REVERT: C 125 LYS cc_start: 0.8631 (tttp) cc_final: 0.8034 (tptp) REVERT: a 282 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7665 (ttp80) REVERT: a 379 ARG cc_start: 0.7044 (ttp-110) cc_final: 0.6735 (mtm110) REVERT: b 270 GLU cc_start: 0.6096 (mm-30) cc_final: 0.4298 (tm-30) REVERT: b 304 LYS cc_start: 0.8446 (mmtt) cc_final: 0.8019 (mmtm) REVERT: b 321 GLN cc_start: 0.8491 (mm110) cc_final: 0.8209 (mm110) REVERT: b 379 ARG cc_start: 0.8283 (ttm110) cc_final: 0.6598 (tmm160) REVERT: b 384 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8276 (mtmt) outliers start: 16 outliers final: 5 residues processed: 186 average time/residue: 1.4132 time to fit residues: 280.5156 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 : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain c residue 295 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 96 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.146967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122743 restraints weight = 11461.107| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.92 r_work: 0.3223 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10741 Z= 0.135 Angle : 0.635 8.216 14735 Z= 0.293 Chirality : 0.041 0.254 1878 Planarity : 0.004 0.047 1748 Dihedral : 8.235 66.766 2894 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.04 % Allowed : 8.71 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1017 helix: 0.53 (0.28), residues: 345 sheet: 0.46 (0.43), residues: 144 loop : 0.01 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 PHE 0.009 0.001 PHE C 157 TYR 0.010 0.001 TYR C 253 ARG 0.008 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 33) link_NAG-ASN : angle 2.24601 ( 99) link_ALPHA1-6 : bond 0.00626 ( 1) link_ALPHA1-6 : angle 1.25722 ( 3) link_BETA1-4 : bond 0.00437 ( 32) link_BETA1-4 : angle 2.15412 ( 96) link_ALPHA1-2 : bond 0.00372 ( 2) link_ALPHA1-2 : angle 1.88244 ( 6) link_ALPHA1-3 : bond 0.01223 ( 3) link_ALPHA1-3 : angle 1.35277 ( 9) hydrogen bonds : bond 0.03649 ( 411) hydrogen bonds : angle 4.66616 ( 1113) link_BETA1-6 : bond 0.00334 ( 5) link_BETA1-6 : angle 1.27092 ( 15) SS BOND : bond 0.00388 ( 21) SS BOND : angle 1.67405 ( 42) covalent geometry : bond 0.00310 (10644) covalent geometry : angle 0.57725 (14465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7979 (mp) REVERT: C 67 GLU cc_start: 0.8607 (tt0) cc_final: 0.8357 (tt0) REVERT: C 125 LYS cc_start: 0.8628 (tttp) cc_final: 0.8010 (tptp) REVERT: a 379 ARG cc_start: 0.7072 (ttp-110) cc_final: 0.6760 (mtm110) REVERT: b 270 GLU cc_start: 0.6082 (mm-30) cc_final: 0.4201 (tm-30) REVERT: b 304 LYS cc_start: 0.8441 (mmtt) cc_final: 0.7996 (mmtm) REVERT: b 321 GLN cc_start: 0.8476 (mm110) cc_final: 0.8182 (mm110) REVERT: b 379 ARG cc_start: 0.8258 (ttm110) cc_final: 0.6540 (tmm160) REVERT: c 332 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7899 (ttt) outliers start: 19 outliers final: 7 residues processed: 179 average time/residue: 1.2405 time to fit residues: 238.1668 Evaluate side-chains 165 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 333 SER Chi-restraints excluded: chain c residue 332 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 338 ASN b 354 HIS c 342 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.117457 restraints weight = 11387.482| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.92 r_work: 0.3154 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10741 Z= 0.219 Angle : 0.730 7.963 14735 Z= 0.335 Chirality : 0.044 0.283 1878 Planarity : 0.004 0.048 1748 Dihedral : 7.575 66.489 2894 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.12 % Allowed : 9.46 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1017 helix: 0.32 (0.28), residues: 345 sheet: 0.51 (0.41), residues: 132 loop : -0.09 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP c 283 HIS 0.008 0.002 HIS A 230 PHE 0.013 0.002 PHE B 117 TYR 0.015 0.002 TYR B 66 ARG 0.010 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 33) link_NAG-ASN : angle 2.50731 ( 99) link_ALPHA1-6 : bond 0.00756 ( 1) link_ALPHA1-6 : angle 1.03632 ( 3) link_BETA1-4 : bond 0.00353 ( 32) link_BETA1-4 : angle 2.45223 ( 96) link_ALPHA1-2 : bond 0.00296 ( 2) link_ALPHA1-2 : angle 1.88904 ( 6) link_ALPHA1-3 : bond 0.01106 ( 3) link_ALPHA1-3 : angle 1.55833 ( 9) hydrogen bonds : bond 0.04141 ( 411) hydrogen bonds : angle 4.88798 ( 1113) link_BETA1-6 : bond 0.00260 ( 5) link_BETA1-6 : angle 1.24341 ( 15) SS BOND : bond 0.00470 ( 21) SS BOND : angle 2.08941 ( 42) covalent geometry : bond 0.00525 (10644) covalent geometry : angle 0.66465 (14465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8054 (mp) REVERT: B 67 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: C 82 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7719 (mtm) REVERT: C 125 LYS cc_start: 0.8683 (tttp) cc_final: 0.8063 (tptp) REVERT: a 332 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.6898 (tpt) REVERT: b 273 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8203 (p0) REVERT: b 304 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8058 (mmtm) REVERT: b 321 GLN cc_start: 0.8499 (mm110) cc_final: 0.8233 (mm110) REVERT: b 379 ARG cc_start: 0.8320 (ttm110) cc_final: 0.6571 (tmm160) REVERT: b 384 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8343 (mtmt) REVERT: c 270 GLU cc_start: 0.6113 (tp30) cc_final: 0.5519 (mm-30) outliers start: 29 outliers final: 10 residues processed: 165 average time/residue: 1.8852 time to fit residues: 334.2916 Evaluate side-chains 166 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 67 GLU 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 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 Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN a 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.119966 restraints weight = 11331.675| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.91 r_work: 0.3188 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10741 Z= 0.141 Angle : 0.635 8.501 14735 Z= 0.294 Chirality : 0.040 0.245 1878 Planarity : 0.003 0.049 1748 Dihedral : 6.848 62.945 2894 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.26 % Allowed : 10.65 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1017 helix: 0.48 (0.28), residues: 345 sheet: 0.62 (0.41), residues: 132 loop : -0.08 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 283 HIS 0.007 0.001 HIS A 230 PHE 0.008 0.001 PHE A 191 TYR 0.014 0.001 TYR B 66 ARG 0.010 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 33) link_NAG-ASN : angle 2.33407 ( 99) link_ALPHA1-6 : bond 0.00735 ( 1) link_ALPHA1-6 : angle 1.29028 ( 3) link_BETA1-4 : bond 0.00408 ( 32) link_BETA1-4 : angle 2.13209 ( 96) link_ALPHA1-2 : bond 0.00326 ( 2) link_ALPHA1-2 : angle 1.81483 ( 6) link_ALPHA1-3 : bond 0.01137 ( 3) link_ALPHA1-3 : angle 1.31598 ( 9) hydrogen bonds : bond 0.03528 ( 411) hydrogen bonds : angle 4.65953 ( 1113) link_BETA1-6 : bond 0.00237 ( 5) link_BETA1-6 : angle 1.27286 ( 15) SS BOND : bond 0.00415 ( 21) SS BOND : angle 1.64943 ( 42) covalent geometry : bond 0.00328 (10644) covalent geometry : angle 0.57497 (14465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7983 (mp) REVERT: A 250 ARG cc_start: 0.7925 (ttt90) cc_final: 0.7702 (tpt170) REVERT: C 60 SER cc_start: 0.5885 (t) cc_final: 0.5652 (m) REVERT: C 125 LYS cc_start: 0.8666 (tttp) cc_final: 0.8066 (tptp) REVERT: a 332 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.6854 (tpt) REVERT: b 270 GLU cc_start: 0.6001 (mm-30) cc_final: 0.5646 (mm-30) REVERT: b 273 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8193 (p0) REVERT: b 304 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8046 (mmtm) REVERT: b 321 GLN cc_start: 0.8473 (mm110) cc_final: 0.8210 (mm110) REVERT: b 379 ARG cc_start: 0.8321 (ttm110) cc_final: 0.6649 (tmm160) REVERT: b 412 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7912 (p) REVERT: c 270 GLU cc_start: 0.5989 (tp30) cc_final: 0.4917 (mm-30) outliers start: 21 outliers final: 12 residues processed: 170 average time/residue: 1.4102 time to fit residues: 255.9940 Evaluate side-chains 164 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN a 324 GLN b 331 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120181 restraints weight = 11365.047| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.96 r_work: 0.3185 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10741 Z= 0.147 Angle : 0.631 9.229 14735 Z= 0.292 Chirality : 0.040 0.240 1878 Planarity : 0.003 0.045 1748 Dihedral : 6.335 62.481 2894 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.23 % Allowed : 10.75 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1017 helix: 0.56 (0.28), residues: 345 sheet: 0.72 (0.41), residues: 132 loop : -0.09 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.010 0.002 PHE B 191 TYR 0.014 0.001 TYR B 66 ARG 0.005 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 33) link_NAG-ASN : angle 2.28793 ( 99) link_ALPHA1-6 : bond 0.00786 ( 1) link_ALPHA1-6 : angle 1.26928 ( 3) link_BETA1-4 : bond 0.00398 ( 32) link_BETA1-4 : angle 2.10056 ( 96) link_ALPHA1-2 : bond 0.00279 ( 2) link_ALPHA1-2 : angle 1.82845 ( 6) link_ALPHA1-3 : bond 0.01020 ( 3) link_ALPHA1-3 : angle 1.28893 ( 9) hydrogen bonds : bond 0.03483 ( 411) hydrogen bonds : angle 4.57955 ( 1113) link_BETA1-6 : bond 0.00235 ( 5) link_BETA1-6 : angle 1.29220 ( 15) SS BOND : bond 0.00405 ( 21) SS BOND : angle 1.60511 ( 42) covalent geometry : bond 0.00345 (10644) covalent geometry : angle 0.57314 (14465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7984 (mp) REVERT: C 60 SER cc_start: 0.5949 (t) cc_final: 0.5734 (m) REVERT: C 95 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8411 (tt) REVERT: C 125 LYS cc_start: 0.8679 (tttp) cc_final: 0.8069 (tptp) REVERT: C 251 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8156 (t0) REVERT: a 332 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.6825 (tpt) REVERT: b 273 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8244 (p0) REVERT: b 291 LYS cc_start: 0.8627 (mttm) cc_final: 0.8392 (mttm) REVERT: b 304 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8035 (mmtm) REVERT: b 321 GLN cc_start: 0.8519 (mm110) cc_final: 0.8250 (mm110) REVERT: b 379 ARG cc_start: 0.8321 (ttm110) cc_final: 0.6745 (tmm160) REVERT: b 384 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8290 (mtmt) REVERT: b 412 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7933 (p) REVERT: c 270 GLU cc_start: 0.6117 (tp30) cc_final: 0.4952 (mm-30) outliers start: 30 outliers final: 15 residues processed: 167 average time/residue: 1.7410 time to fit residues: 310.6758 Evaluate side-chains 171 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 95 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 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 341 VAL Chi-restraints excluded: chain b residue 384 LYS Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 116 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN B 189 GLN a 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119984 restraints weight = 11456.010| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.94 r_work: 0.3222 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10741 Z= 0.149 Angle : 0.626 7.781 14735 Z= 0.290 Chirality : 0.040 0.236 1878 Planarity : 0.003 0.056 1748 Dihedral : 6.279 62.424 2894 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.44 % Allowed : 11.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1017 helix: 0.57 (0.28), residues: 345 sheet: 0.77 (0.41), residues: 132 loop : -0.10 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.009 0.002 PHE B 191 TYR 0.012 0.001 TYR B 66 ARG 0.012 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 33) link_NAG-ASN : angle 2.28786 ( 99) link_ALPHA1-6 : bond 0.00800 ( 1) link_ALPHA1-6 : angle 1.27384 ( 3) link_BETA1-4 : bond 0.00395 ( 32) link_BETA1-4 : angle 2.07780 ( 96) link_ALPHA1-2 : bond 0.00244 ( 2) link_ALPHA1-2 : angle 1.81340 ( 6) link_ALPHA1-3 : bond 0.01011 ( 3) link_ALPHA1-3 : angle 1.25845 ( 9) hydrogen bonds : bond 0.03468 ( 411) hydrogen bonds : angle 4.56726 ( 1113) link_BETA1-6 : bond 0.00232 ( 5) link_BETA1-6 : angle 1.28531 ( 15) SS BOND : bond 0.00415 ( 21) SS BOND : angle 1.47846 ( 42) covalent geometry : bond 0.00352 (10644) covalent geometry : angle 0.56972 (14465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7984 (mp) REVERT: A 192 MET cc_start: 0.7967 (mmp) cc_final: 0.7251 (mmt) REVERT: C 60 SER cc_start: 0.5914 (t) cc_final: 0.5708 (m) REVERT: C 125 LYS cc_start: 0.8681 (tttp) cc_final: 0.8067 (tptp) REVERT: C 251 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8174 (t0) REVERT: a 332 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.6817 (tpt) REVERT: b 273 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8245 (p0) REVERT: b 291 LYS cc_start: 0.8641 (mttm) cc_final: 0.8386 (mttm) REVERT: b 304 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8031 (mmtm) REVERT: b 321 GLN cc_start: 0.8513 (mm110) cc_final: 0.8252 (mm110) REVERT: b 379 ARG cc_start: 0.8329 (ttm110) cc_final: 0.6768 (tmm160) REVERT: b 384 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8285 (mtmt) REVERT: b 412 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7936 (p) REVERT: c 270 GLU cc_start: 0.6105 (tp30) cc_final: 0.5474 (mm-30) outliers start: 32 outliers final: 18 residues processed: 174 average time/residue: 1.5167 time to fit residues: 282.9972 Evaluate side-chains 174 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 B residue 231 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 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 295 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 94 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 209 ASN B 189 GLN B 218 GLN B 247 GLN a 324 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115686 restraints weight = 11516.569| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.94 r_work: 0.3165 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10741 Z= 0.276 Angle : 0.787 11.687 14735 Z= 0.359 Chirality : 0.046 0.295 1878 Planarity : 0.004 0.065 1748 Dihedral : 7.165 65.930 2894 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.66 % Allowed : 11.51 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1017 helix: 0.21 (0.28), residues: 345 sheet: 0.72 (0.41), residues: 132 loop : -0.23 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 283 HIS 0.008 0.001 HIS A 230 PHE 0.013 0.002 PHE B 233 TYR 0.019 0.002 TYR B 66 ARG 0.013 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 33) link_NAG-ASN : angle 2.63275 ( 99) link_ALPHA1-6 : bond 0.00800 ( 1) link_ALPHA1-6 : angle 1.01669 ( 3) link_BETA1-4 : bond 0.00388 ( 32) link_BETA1-4 : angle 2.51158 ( 96) link_ALPHA1-2 : bond 0.00143 ( 2) link_ALPHA1-2 : angle 1.84477 ( 6) link_ALPHA1-3 : bond 0.00914 ( 3) link_ALPHA1-3 : angle 1.45519 ( 9) hydrogen bonds : bond 0.04451 ( 411) hydrogen bonds : angle 4.91963 ( 1113) link_BETA1-6 : bond 0.00197 ( 5) link_BETA1-6 : angle 1.31871 ( 15) SS BOND : bond 0.00673 ( 21) SS BOND : angle 2.27876 ( 42) covalent geometry : bond 0.00667 (10644) covalent geometry : angle 0.72208 (14465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8155 (mp) REVERT: C 82 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7736 (mtm) REVERT: C 125 LYS cc_start: 0.8723 (tttp) cc_final: 0.8088 (tptp) REVERT: C 251 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8046 (t0) REVERT: a 332 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.6888 (tpt) REVERT: b 304 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8157 (mmtm) REVERT: b 321 GLN cc_start: 0.8542 (mm110) cc_final: 0.8279 (mm110) REVERT: b 379 ARG cc_start: 0.8332 (ttm110) cc_final: 0.6756 (tmm160) REVERT: b 384 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8385 (mtmt) REVERT: b 412 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7954 (p) REVERT: c 270 GLU cc_start: 0.6223 (tp30) cc_final: 0.5637 (mm-30) outliers start: 34 outliers final: 21 residues processed: 164 average time/residue: 1.7573 time to fit residues: 309.3848 Evaluate side-chains 170 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 C residue 82 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 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 384 LYS Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 302 ASN Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 109 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 c 354 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.120694 restraints weight = 11446.633| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.95 r_work: 0.3197 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 : 0.003 0.040 10741 Z= 0.118 Angle : 0.611 9.900 14735 Z= 0.285 Chirality : 0.039 0.215 1878 Planarity : 0.003 0.058 1748 Dihedral : 6.281 61.743 2894 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.58 % Allowed : 12.47 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1017 helix: 0.62 (0.28), residues: 342 sheet: 0.89 (0.42), residues: 132 loop : -0.13 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 283 HIS 0.006 0.001 HIS A 230 PHE 0.008 0.001 PHE b 309 TYR 0.010 0.001 TYR B 66 ARG 0.015 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 33) link_NAG-ASN : angle 2.26913 ( 99) link_ALPHA1-6 : bond 0.00776 ( 1) link_ALPHA1-6 : angle 1.38047 ( 3) link_BETA1-4 : bond 0.00433 ( 32) link_BETA1-4 : angle 1.94089 ( 96) link_ALPHA1-2 : bond 0.00268 ( 2) link_ALPHA1-2 : angle 1.71789 ( 6) link_ALPHA1-3 : bond 0.01118 ( 3) link_ALPHA1-3 : angle 1.19377 ( 9) hydrogen bonds : bond 0.03288 ( 411) hydrogen bonds : angle 4.51354 ( 1113) link_BETA1-6 : bond 0.00228 ( 5) link_BETA1-6 : angle 1.29736 ( 15) SS BOND : bond 0.00428 ( 21) SS BOND : angle 1.38882 ( 42) covalent geometry : bond 0.00267 (10644) covalent geometry : angle 0.55677 (14465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8039 (mp) REVERT: C 82 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7646 (mtm) REVERT: C 125 LYS cc_start: 0.8697 (tttp) cc_final: 0.8066 (tptp) REVERT: b 291 LYS cc_start: 0.8536 (mttm) cc_final: 0.8218 (mttm) REVERT: b 304 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8113 (mmtm) REVERT: b 321 GLN cc_start: 0.8504 (mm110) cc_final: 0.8238 (mm110) REVERT: b 379 ARG cc_start: 0.8310 (ttm110) cc_final: 0.6779 (tmm160) REVERT: b 412 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7895 (p) REVERT: c 270 GLU cc_start: 0.6064 (tp30) cc_final: 0.5410 (mm-30) outliers start: 24 outliers final: 18 residues processed: 164 average time/residue: 1.3154 time to fit residues: 231.4698 Evaluate side-chains 166 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 A residue 213 ILE Chi-restraints excluded: chain B residue 192 MET 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 a residue 274 THR Chi-restraints excluded: chain a residue 333 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 70 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 3 optimal weight: 0.0070 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 c 354 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122036 restraints weight = 11321.333| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.92 r_work: 0.3217 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 10741 Z= 0.118 Angle : 0.630 12.712 14735 Z= 0.295 Chirality : 0.039 0.319 1878 Planarity : 0.003 0.067 1748 Dihedral : 6.076 62.086 2894 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.15 % Allowed : 13.01 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1017 helix: 0.71 (0.28), residues: 342 sheet: 0.96 (0.42), residues: 132 loop : -0.10 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 283 HIS 0.005 0.001 HIS A 230 PHE 0.008 0.001 PHE b 309 TYR 0.012 0.001 TYR B 66 ARG 0.015 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 33) link_NAG-ASN : angle 2.21177 ( 99) link_ALPHA1-6 : bond 0.00819 ( 1) link_ALPHA1-6 : angle 1.39773 ( 3) link_BETA1-4 : bond 0.00438 ( 32) link_BETA1-4 : angle 1.89626 ( 96) link_ALPHA1-2 : bond 0.00133 ( 2) link_ALPHA1-2 : angle 1.73620 ( 6) link_ALPHA1-3 : bond 0.01005 ( 3) link_ALPHA1-3 : angle 1.16375 ( 9) hydrogen bonds : bond 0.03273 ( 411) hydrogen bonds : angle 4.46280 ( 1113) link_BETA1-6 : bond 0.00287 ( 5) link_BETA1-6 : angle 1.27486 ( 15) SS BOND : bond 0.00577 ( 21) SS BOND : angle 2.04697 ( 42) covalent geometry : bond 0.00277 (10644) covalent geometry : angle 0.57451 (14465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8008 (mp) REVERT: C 67 GLU cc_start: 0.8585 (tt0) cc_final: 0.8348 (tt0) REVERT: C 101 THR cc_start: 0.9126 (m) cc_final: 0.8806 (p) REVERT: C 125 LYS cc_start: 0.8691 (tttp) cc_final: 0.8077 (tptp) REVERT: b 304 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8102 (mmtm) REVERT: b 321 GLN cc_start: 0.8511 (mm110) cc_final: 0.8250 (mm110) REVERT: b 379 ARG cc_start: 0.8304 (ttm110) cc_final: 0.6765 (tmm160) REVERT: c 270 GLU cc_start: 0.6072 (tp30) cc_final: 0.4894 (mm-30) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 1.6351 time to fit residues: 280.9506 Evaluate side-chains 163 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 333 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 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 86 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 111 optimal weight: 0.0060 chunk 46 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 230 HIS a 324 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122932 restraints weight = 11286.827| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.92 r_work: 0.3230 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10741 Z= 0.114 Angle : 0.608 14.255 14735 Z= 0.286 Chirality : 0.039 0.306 1878 Planarity : 0.003 0.057 1748 Dihedral : 5.807 62.195 2894 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.94 % Allowed : 13.33 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.27), residues: 1017 helix: 0.79 (0.29), residues: 342 sheet: 1.04 (0.42), residues: 132 loop : -0.10 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 283 HIS 0.005 0.001 HIS A 230 PHE 0.007 0.001 PHE b 309 TYR 0.012 0.001 TYR B 66 ARG 0.015 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 33) link_NAG-ASN : angle 2.14776 ( 99) link_ALPHA1-6 : bond 0.00879 ( 1) link_ALPHA1-6 : angle 1.43212 ( 3) link_BETA1-4 : bond 0.00421 ( 32) link_BETA1-4 : angle 1.82085 ( 96) link_ALPHA1-2 : bond 0.00229 ( 2) link_ALPHA1-2 : angle 1.73530 ( 6) link_ALPHA1-3 : bond 0.01051 ( 3) link_ALPHA1-3 : angle 1.18627 ( 9) hydrogen bonds : bond 0.03201 ( 411) hydrogen bonds : angle 4.38672 ( 1113) link_BETA1-6 : bond 0.00287 ( 5) link_BETA1-6 : angle 1.26456 ( 15) SS BOND : bond 0.00538 ( 21) SS BOND : angle 1.80227 ( 42) covalent geometry : bond 0.00264 (10644) covalent geometry : angle 0.55568 (14465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9450.74 seconds wall clock time: 172 minutes 46.64 seconds (10366.64 seconds total)