Starting phenix.real_space_refine on Thu Feb 5 12:04:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ln7_63228/02_2026/9ln7_63228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ln7_63228/02_2026/9ln7_63228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ln7_63228/02_2026/9ln7_63228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ln7_63228/02_2026/9ln7_63228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ln7_63228/02_2026/9ln7_63228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ln7_63228/02_2026/9ln7_63228.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.091 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 135 5.16 5 C 10985 2.51 5 N 2740 2.21 5 O 3080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16940 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3268 Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 122 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3268 Chain: "D" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 122 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3268 Chain: "F" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 122 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3268 Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 122 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3268 Chain: "J" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 122 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 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: "I" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.25, per 1000 atoms: 0.37 Number of scatterers: 16940 At special positions: 0 Unit cell: (97.37, 95.23, 163.71, 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 135 16.00 O 3080 8.00 N 2740 7.00 C 10985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 17 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 9 " distance=2.03 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 17 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 9 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 17 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 9 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 212 " - pdb=" SG CYS G 213 " distance=2.04 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 17 " distance=2.03 Simple disulfide: pdb=" SG CYS H 4 " - pdb=" SG CYS H 9 " distance=2.03 Simple disulfide: pdb=" SG CYS I 150 " - pdb=" SG CYS I 164 " distance=2.03 Simple disulfide: pdb=" SG CYS I 212 " - pdb=" SG CYS I 213 " distance=2.04 Simple disulfide: pdb=" SG CYS J 3 " - pdb=" SG CYS J 17 " distance=2.03 Simple disulfide: pdb=" SG CYS J 4 " - pdb=" SG CYS J 9 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 601 " - " ASN A 90 " " NAG C 601 " - " ASN C 90 " " NAG E 601 " - " ASN E 90 " " NAG G 601 " - " ASN G 90 " " NAG I 601 " - " ASN I 90 " " NAG K 1 " - " ASN A 46 " " NAG L 1 " - " ASN A 133 " " NAG M 1 " - " ASN C 46 " " NAG N 1 " - " ASN C 133 " " NAG O 1 " - " ASN E 46 " " NAG P 1 " - " ASN E 133 " " NAG Q 1 " - " ASN G 46 " " NAG R 1 " - " ASN G 133 " " NAG S 1 " - " ASN I 46 " " NAG T 1 " - " ASN I 133 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 1.5 seconds 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 44.5% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.786A pdb=" N LYS A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 260 through 280 Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 432 through 489 Processing helix chain 'A' and resid 492 through 502 Processing helix chain 'B' and resid 7 through 13 removed outlier: 4.048A pdb=" N TRP B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 removed outlier: 3.638A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 237 through 250 Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 260 through 281 removed outlier: 4.155A pdb=" N GLU C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 321 through 325 removed outlier: 4.260A pdb=" N GLY C 325 " --> pdb=" O PRO C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 432 through 490 removed outlier: 4.173A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 502 Processing helix chain 'D' and resid 7 through 13 removed outlier: 4.042A pdb=" N TRP D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.786A pdb=" N LYS E 28 " --> pdb=" O GLU E 24 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 237 through 249 Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 260 through 280 Processing helix chain 'E' and resid 291 through 319 Processing helix chain 'E' and resid 328 through 336 Processing helix chain 'E' and resid 337 through 344 Processing helix chain 'E' and resid 432 through 489 Processing helix chain 'E' and resid 492 through 502 Processing helix chain 'F' and resid 7 through 13 removed outlier: 3.945A pdb=" N TRP F 11 " --> pdb=" O ASN F 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 34 Processing helix chain 'G' and resid 230 through 237 Processing helix chain 'G' and resid 237 through 250 Processing helix chain 'G' and resid 251 through 254 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.522A pdb=" N GLY G 259 " --> pdb=" O ALA G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 280 Processing helix chain 'G' and resid 291 through 319 Processing helix chain 'G' and resid 328 through 336 Processing helix chain 'G' and resid 337 through 343 Processing helix chain 'G' and resid 432 through 490 removed outlier: 4.005A pdb=" N ALA G 490 " --> pdb=" O ILE G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 502 Processing helix chain 'H' and resid 7 through 13 removed outlier: 3.868A pdb=" N TRP H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 34 removed outlier: 3.594A pdb=" N VAL I 34 " --> pdb=" O TYR I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 237 Processing helix chain 'I' and resid 237 through 250 Processing helix chain 'I' and resid 251 through 254 Processing helix chain 'I' and resid 255 through 259 removed outlier: 3.538A pdb=" N SER I 258 " --> pdb=" O PRO I 255 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY I 259 " --> pdb=" O ALA I 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 255 through 259' Processing helix chain 'I' and resid 260 through 280 Processing helix chain 'I' and resid 291 through 319 Processing helix chain 'I' and resid 328 through 336 Processing helix chain 'I' and resid 337 through 344 Processing helix chain 'I' and resid 432 through 489 Processing helix chain 'I' and resid 492 through 502 Processing helix chain 'J' and resid 7 through 13 removed outlier: 4.127A pdb=" N TRP J 11 " --> pdb=" O ASN J 7 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 102 removed outlier: 4.300A pdb=" N HIS A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 102 removed outlier: 4.300A pdb=" N HIS A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 71 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP A 64 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR A 73 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE A 62 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN A 75 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR A 83 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A 52 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.813A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.813A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU A 215 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N TYR A 210 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 208 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.807A pdb=" N ASN C 133 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.807A pdb=" N ASN C 133 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN C 75 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE C 62 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N TRP C 77 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU C 60 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN C 79 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER C 58 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER C 81 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N SER C 56 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N THR C 83 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N TYR C 54 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.752A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.752A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG C 208 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 143 through 149 removed outlier: 6.768A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLN E 79 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N SER E 58 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER E 81 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N SER E 56 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 99 through 102 Processing sheet with id=AB2, first strand: chain 'E' and resid 161 through 167 removed outlier: 7.028A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.190A pdb=" N GLU E 215 " --> pdb=" O TYR E 210 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR E 210 " --> pdb=" O GLU E 215 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG E 208 " --> pdb=" O TYR E 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 99 through 102 removed outlier: 4.279A pdb=" N HIS G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 99 through 102 removed outlier: 4.279A pdb=" N HIS G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN G 75 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE G 62 " --> pdb=" O ASN G 75 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N TRP G 77 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU G 60 " --> pdb=" O TRP G 77 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLN G 79 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER G 58 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N SER G 81 " --> pdb=" O SER G 56 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N SER G 56 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N THR G 83 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N TYR G 54 " --> pdb=" O THR G 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 112 through 114 removed outlier: 4.785A pdb=" N SER G 170 " --> pdb=" O PRO G 218 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR G 225 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 112 through 114 removed outlier: 4.785A pdb=" N SER G 170 " --> pdb=" O PRO G 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 99 through 102 removed outlier: 4.353A pdb=" N HIS I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 99 through 102 removed outlier: 4.353A pdb=" N HIS I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL I 71 " --> pdb=" O ASP I 64 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP I 64 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR I 73 " --> pdb=" O ILE I 62 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE I 62 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN I 75 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR I 83 " --> pdb=" O THR I 52 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR I 52 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU I 51 " --> pdb=" O ASP I 179 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLN I 181 " --> pdb=" O LEU I 51 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL I 53 " --> pdb=" O GLN I 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 161 through 168 removed outlier: 3.521A pdb=" N VAL I 220 " --> pdb=" O PHE I 168 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR I 225 " --> pdb=" O VAL I 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 161 through 168 removed outlier: 3.521A pdb=" N VAL I 220 " --> pdb=" O PHE I 168 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2802 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: 2.91 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5238 1.34 - 1.47: 4637 1.47 - 1.60: 7340 1.60 - 1.72: 0 1.72 - 1.85: 190 Bond restraints: 17405 Sorted by residual: bond pdb=" C ARG C 208 " pdb=" N PHE C 209 " ideal model delta sigma weight residual 1.330 1.380 -0.049 1.45e-02 4.76e+03 1.16e+01 bond pdb=" C TYR G 210 " pdb=" N GLU G 211 " ideal model delta sigma weight residual 1.335 1.379 -0.044 1.35e-02 5.49e+03 1.06e+01 bond pdb=" C PHE E 209 " pdb=" N TYR E 210 " ideal model delta sigma weight residual 1.331 1.289 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" C TYR E 217 " pdb=" N PRO E 218 " ideal model delta sigma weight residual 1.331 1.288 0.042 1.31e-02 5.83e+03 1.04e+01 bond pdb=" C PHE I 209 " pdb=" N TYR I 210 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.37e-02 5.33e+03 6.35e+00 ... (remaining 17400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 23177 1.76 - 3.52: 502 3.52 - 5.29: 52 5.29 - 7.05: 8 7.05 - 8.81: 1 Bond angle restraints: 23740 Sorted by residual: angle pdb=" N GLU A 438 " pdb=" CA GLU A 438 " pdb=" CB GLU A 438 " ideal model delta sigma weight residual 110.16 115.75 -5.59 1.48e+00 4.57e-01 1.43e+01 angle pdb=" N VAL C 154 " pdb=" CA VAL C 154 " pdb=" C VAL C 154 " ideal model delta sigma weight residual 111.91 108.63 3.28 8.90e-01 1.26e+00 1.36e+01 angle pdb=" CA ASN E 492 " pdb=" CB ASN E 492 " pdb=" CG ASN E 492 " ideal model delta sigma weight residual 112.60 115.40 -2.80 1.00e+00 1.00e+00 7.83e+00 angle pdb=" C PRO E 491 " pdb=" N ASN E 492 " pdb=" CA ASN E 492 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.32e+00 angle pdb=" NE ARG E 101 " pdb=" CZ ARG E 101 " pdb=" NH2 ARG E 101 " ideal model delta sigma weight residual 119.20 121.55 -2.35 9.00e-01 1.23e+00 6.81e+00 ... (remaining 23735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 9595 17.79 - 35.58: 818 35.58 - 53.37: 133 53.37 - 71.15: 21 71.15 - 88.94: 13 Dihedral angle restraints: 10580 sinusoidal: 4490 harmonic: 6090 Sorted by residual: dihedral pdb=" CB CYS F 3 " pdb=" SG CYS F 3 " pdb=" SG CYS F 17 " pdb=" CB CYS F 17 " ideal model delta sinusoidal sigma weight residual -86.00 -165.42 79.42 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS D 3 " pdb=" SG CYS D 3 " pdb=" SG CYS D 17 " pdb=" CB CYS D 17 " ideal model delta sinusoidal sigma weight residual -86.00 -158.18 72.18 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS B 3 " pdb=" SG CYS B 3 " pdb=" SG CYS B 17 " pdb=" CB CYS B 17 " ideal model delta sinusoidal sigma weight residual -86.00 -150.34 64.34 1 1.00e+01 1.00e-02 5.44e+01 ... (remaining 10577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1945 0.041 - 0.081: 581 0.081 - 0.122: 171 0.122 - 0.162: 28 0.162 - 0.203: 5 Chirality restraints: 2730 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.74e+00 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.91e+00 chirality pdb=" CB ILE E 201 " pdb=" CA ILE E 201 " pdb=" CG1 ILE E 201 " pdb=" CG2 ILE E 201 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2727 not shown) Planarity restraints: 2950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 290 " -0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO G 291 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO G 291 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 291 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 157 " -0.045 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO G 158 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 158 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 158 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET G 283 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.15e+00 pdb=" N PRO G 284 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 284 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 284 " 0.037 5.00e-02 4.00e+02 ... (remaining 2947 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 656 2.72 - 3.27: 16624 3.27 - 3.81: 28755 3.81 - 4.36: 33573 4.36 - 4.90: 60132 Nonbonded interactions: 139740 Sorted by model distance: nonbonded pdb=" SG CYS I 212 " pdb=" NH2 ARG J 10 " model vdw 2.179 3.480 nonbonded pdb=" OG1 THR E 230 " pdb=" OD2 ASP E 500 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP A 451 " pdb=" NH1 ARG I 446 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR C 230 " pdb=" OD2 ASP C 500 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR A 230 " pdb=" OD2 ASP A 500 " model vdw 2.287 3.040 ... (remaining 139735 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 136 or resid 138 through 601)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 601)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 601)) selection = (chain 'G' and (resid 23 through 136 or resid 138 through 601)) selection = (chain 'I' and (resid 23 through 136 or resid 138 through 601)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.790 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.004 0.049 17450 Z= 0.188 Angle : 0.591 8.810 23855 Z= 0.297 Chirality : 0.043 0.203 2730 Planarity : 0.005 0.077 2935 Dihedral : 12.878 88.942 6580 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.05 % Allowed : 0.44 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 2045 helix: 1.25 (0.17), residues: 890 sheet: -0.76 (0.24), residues: 430 loop : -0.24 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 101 TYR 0.012 0.001 TYR C 442 PHE 0.015 0.001 PHE A 297 TRP 0.020 0.001 TRP C 341 HIS 0.004 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00413 (17405) covalent geometry : angle 0.58483 (23740) SS BOND : bond 0.00606 ( 20) SS BOND : angle 1.40621 ( 40) hydrogen bonds : bond 0.11972 ( 873) hydrogen bonds : angle 6.09862 ( 2802) link_BETA1-4 : bond 0.00293 ( 10) link_BETA1-4 : angle 0.87550 ( 30) link_NAG-ASN : bond 0.00120 ( 15) link_NAG-ASN : angle 1.46286 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: I 452 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7429 (mp0) outliers start: 1 outliers final: 2 residues processed: 249 average time/residue: 0.4380 time to fit residues: 124.6236 Evaluate side-chains 203 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain G residue 480 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.6296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.091361 restraints weight = 38114.801| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.16 r_work: 0.2910 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17450 Z= 0.122 Angle : 0.556 8.155 23855 Z= 0.279 Chirality : 0.042 0.177 2730 Planarity : 0.005 0.065 2935 Dihedral : 5.691 51.333 2773 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.48 % Allowed : 7.43 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2045 helix: 1.46 (0.17), residues: 890 sheet: -0.95 (0.23), residues: 460 loop : 0.05 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 441 TYR 0.011 0.001 TYR C 442 PHE 0.011 0.001 PHE A 297 TRP 0.015 0.001 TRP C 341 HIS 0.005 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00285 (17405) covalent geometry : angle 0.54683 (23740) SS BOND : bond 0.00658 ( 20) SS BOND : angle 1.99546 ( 40) hydrogen bonds : bond 0.03641 ( 873) hydrogen bonds : angle 4.66009 ( 2802) link_BETA1-4 : bond 0.00123 ( 10) link_BETA1-4 : angle 0.94765 ( 30) link_NAG-ASN : bond 0.00205 ( 15) link_NAG-ASN : angle 1.40528 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8586 (t0) cc_final: 0.8015 (t0) REVERT: A 120 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: A 441 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7531 (ptp-110) REVERT: E 238 LEU cc_start: 0.7659 (tp) cc_final: 0.7322 (mm) REVERT: G 66 ASP cc_start: 0.8125 (t0) cc_final: 0.7539 (t0) REVERT: I 64 ASP cc_start: 0.8480 (t0) cc_final: 0.8149 (t0) outliers start: 27 outliers final: 9 residues processed: 231 average time/residue: 0.4288 time to fit residues: 113.7970 Evaluate side-chains 217 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain I residue 336 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 167 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 137 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.089307 restraints weight = 41081.771| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.24 r_work: 0.2874 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 17450 Z= 0.162 Angle : 0.577 13.857 23855 Z= 0.284 Chirality : 0.043 0.273 2730 Planarity : 0.004 0.058 2935 Dihedral : 5.294 65.801 2770 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.08 % Allowed : 8.20 % Favored : 89.73 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2045 helix: 1.58 (0.17), residues: 860 sheet: -0.86 (0.23), residues: 430 loop : -0.09 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 441 TYR 0.012 0.001 TYR C 442 PHE 0.019 0.001 PHE I 297 TRP 0.013 0.001 TRP C 341 HIS 0.006 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00395 (17405) covalent geometry : angle 0.56225 (23740) SS BOND : bond 0.00760 ( 20) SS BOND : angle 2.73506 ( 40) hydrogen bonds : bond 0.03611 ( 873) hydrogen bonds : angle 4.51358 ( 2802) link_BETA1-4 : bond 0.00126 ( 10) link_BETA1-4 : angle 0.96739 ( 30) link_NAG-ASN : bond 0.00223 ( 15) link_NAG-ASN : angle 1.52845 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.407 Fit side-chains REVERT: A 64 ASP cc_start: 0.8691 (t0) cc_final: 0.8113 (t0) REVERT: A 441 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7408 (ptp-110) REVERT: C 317 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7417 (t80) REVERT: E 160 ASP cc_start: 0.8361 (m-30) cc_final: 0.8082 (m-30) REVERT: E 238 LEU cc_start: 0.7674 (tp) cc_final: 0.7323 (mm) REVERT: G 66 ASP cc_start: 0.8117 (t0) cc_final: 0.7546 (t0) REVERT: G 160 ASP cc_start: 0.8444 (m-30) cc_final: 0.8028 (m-30) REVERT: I 64 ASP cc_start: 0.8512 (t0) cc_final: 0.8298 (t0) REVERT: I 283 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7479 (ttt) outliers start: 38 outliers final: 16 residues processed: 223 average time/residue: 0.4374 time to fit residues: 111.7426 Evaluate side-chains 226 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 31 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 492 ASN ** I 137 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.089480 restraints weight = 39603.278| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.19 r_work: 0.2877 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17450 Z= 0.142 Angle : 0.552 9.012 23855 Z= 0.273 Chirality : 0.042 0.220 2730 Planarity : 0.004 0.054 2935 Dihedral : 4.853 64.644 2770 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.91 % Allowed : 9.23 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2045 helix: 1.54 (0.16), residues: 890 sheet: -0.79 (0.23), residues: 425 loop : -0.05 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 441 TYR 0.010 0.001 TYR C 442 PHE 0.013 0.001 PHE A 297 TRP 0.010 0.001 TRP C 341 HIS 0.005 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00345 (17405) covalent geometry : angle 0.53880 (23740) SS BOND : bond 0.00822 ( 20) SS BOND : angle 2.44984 ( 40) hydrogen bonds : bond 0.03466 ( 873) hydrogen bonds : angle 4.40970 ( 2802) link_BETA1-4 : bond 0.00193 ( 10) link_BETA1-4 : angle 0.93585 ( 30) link_NAG-ASN : bond 0.00155 ( 15) link_NAG-ASN : angle 1.53065 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 0.490 Fit side-chains REVERT: A 64 ASP cc_start: 0.8660 (t0) cc_final: 0.8055 (t0) REVERT: A 120 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: A 441 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7381 (mtm110) REVERT: B 7 ASN cc_start: 0.8016 (t0) cc_final: 0.7792 (t160) REVERT: C 317 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7848 (t80) REVERT: E 160 ASP cc_start: 0.8328 (m-30) cc_final: 0.8030 (m-30) REVERT: E 238 LEU cc_start: 0.7631 (tp) cc_final: 0.7271 (mm) REVERT: E 473 MET cc_start: 0.7027 (mtp) cc_final: 0.6240 (ptt) REVERT: G 66 ASP cc_start: 0.8111 (t0) cc_final: 0.7570 (t0) REVERT: G 160 ASP cc_start: 0.8414 (m-30) cc_final: 0.8045 (m-30) REVERT: I 64 ASP cc_start: 0.8462 (t0) cc_final: 0.8188 (t0) REVERT: I 283 MET cc_start: 0.7866 (ttp) cc_final: 0.7465 (ttt) outliers start: 35 outliers final: 14 residues processed: 228 average time/residue: 0.4652 time to fit residues: 122.4876 Evaluate side-chains 229 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 41 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 167 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 ASN D 7 ASN ** I 137 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089171 restraints weight = 33215.096| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.94 r_work: 0.2878 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 17450 Z= 0.152 Angle : 0.561 14.167 23855 Z= 0.275 Chirality : 0.042 0.216 2730 Planarity : 0.004 0.052 2935 Dihedral : 4.596 64.776 2770 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.97 % Allowed : 10.00 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2045 helix: 1.56 (0.16), residues: 890 sheet: -0.81 (0.23), residues: 430 loop : -0.03 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 441 TYR 0.010 0.001 TYR C 442 PHE 0.014 0.001 PHE A 297 TRP 0.009 0.001 TRP C 341 HIS 0.005 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00369 (17405) covalent geometry : angle 0.54828 (23740) SS BOND : bond 0.00814 ( 20) SS BOND : angle 2.45138 ( 40) hydrogen bonds : bond 0.03480 ( 873) hydrogen bonds : angle 4.38885 ( 2802) link_BETA1-4 : bond 0.00164 ( 10) link_BETA1-4 : angle 0.95224 ( 30) link_NAG-ASN : bond 0.00191 ( 15) link_NAG-ASN : angle 1.56716 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.669 Fit side-chains REVERT: A 64 ASP cc_start: 0.8737 (t0) cc_final: 0.8169 (t0) REVERT: A 120 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: A 160 ASP cc_start: 0.8395 (m-30) cc_final: 0.7695 (m-30) REVERT: A 441 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7371 (mtm110) REVERT: C 317 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7956 (t80) REVERT: D 7 ASN cc_start: 0.8210 (t0) cc_final: 0.7968 (t160) REVERT: E 160 ASP cc_start: 0.8496 (m-30) cc_final: 0.7945 (m-30) REVERT: E 238 LEU cc_start: 0.7650 (tp) cc_final: 0.7287 (mm) REVERT: E 473 MET cc_start: 0.7124 (mtp) cc_final: 0.6331 (ptt) REVERT: G 66 ASP cc_start: 0.8080 (t0) cc_final: 0.7568 (t0) REVERT: G 160 ASP cc_start: 0.8536 (m-30) cc_final: 0.8124 (m-30) REVERT: I 64 ASP cc_start: 0.8570 (t0) cc_final: 0.8308 (t0) REVERT: I 283 MET cc_start: 0.7911 (ttp) cc_final: 0.7489 (ttt) outliers start: 36 outliers final: 17 residues processed: 234 average time/residue: 0.4499 time to fit residues: 120.5576 Evaluate side-chains 237 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 37 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 ASN ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.086955 restraints weight = 38109.542| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.08 r_work: 0.2836 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 17450 Z= 0.211 Angle : 0.591 8.765 23855 Z= 0.292 Chirality : 0.044 0.214 2730 Planarity : 0.004 0.051 2935 Dihedral : 4.626 64.546 2770 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.13 % Allowed : 10.60 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2045 helix: 1.56 (0.17), residues: 860 sheet: -0.90 (0.23), residues: 430 loop : -0.08 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 441 TYR 0.012 0.001 TYR E 217 PHE 0.018 0.001 PHE I 297 TRP 0.010 0.001 TRP E 77 HIS 0.005 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00516 (17405) covalent geometry : angle 0.57757 (23740) SS BOND : bond 0.00823 ( 20) SS BOND : angle 2.60827 ( 40) hydrogen bonds : bond 0.03695 ( 873) hydrogen bonds : angle 4.48938 ( 2802) link_BETA1-4 : bond 0.00128 ( 10) link_BETA1-4 : angle 0.95151 ( 30) link_NAG-ASN : bond 0.00323 ( 15) link_NAG-ASN : angle 1.64599 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.592 Fit side-chains REVERT: A 64 ASP cc_start: 0.8647 (t0) cc_final: 0.8053 (t0) REVERT: A 120 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: A 441 ARG cc_start: 0.7721 (mtm110) cc_final: 0.7376 (mtm110) REVERT: E 238 LEU cc_start: 0.7778 (tp) cc_final: 0.7389 (mm) REVERT: G 66 ASP cc_start: 0.8154 (t0) cc_final: 0.7611 (t0) REVERT: I 64 ASP cc_start: 0.8501 (t0) cc_final: 0.8247 (t0) REVERT: I 283 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7708 (ttt) REVERT: I 321 ASP cc_start: 0.8749 (p0) cc_final: 0.8429 (p0) outliers start: 39 outliers final: 20 residues processed: 231 average time/residue: 0.4370 time to fit residues: 115.3157 Evaluate side-chains 236 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 195 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 118 optimal weight: 0.0020 chunk 102 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.087406 restraints weight = 41981.847| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.27 r_work: 0.2841 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 17450 Z= 0.154 Angle : 0.557 8.900 23855 Z= 0.276 Chirality : 0.042 0.217 2730 Planarity : 0.004 0.049 2935 Dihedral : 4.499 64.738 2770 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.02 % Allowed : 11.09 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2045 helix: 1.55 (0.16), residues: 890 sheet: -0.86 (0.23), residues: 430 loop : -0.02 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 441 TYR 0.010 0.001 TYR E 233 PHE 0.014 0.001 PHE A 297 TRP 0.008 0.001 TRP C 341 HIS 0.004 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00375 (17405) covalent geometry : angle 0.54369 (23740) SS BOND : bond 0.00820 ( 20) SS BOND : angle 2.51918 ( 40) hydrogen bonds : bond 0.03537 ( 873) hydrogen bonds : angle 4.41762 ( 2802) link_BETA1-4 : bond 0.00188 ( 10) link_BETA1-4 : angle 0.91341 ( 30) link_NAG-ASN : bond 0.00179 ( 15) link_NAG-ASN : angle 1.57871 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.637 Fit side-chains REVERT: A 64 ASP cc_start: 0.8577 (t0) cc_final: 0.7970 (t0) REVERT: A 120 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: A 441 ARG cc_start: 0.7685 (mtm110) cc_final: 0.7347 (mtm110) REVERT: G 66 ASP cc_start: 0.8126 (t0) cc_final: 0.7587 (t0) REVERT: I 64 ASP cc_start: 0.8488 (t0) cc_final: 0.8234 (t0) REVERT: I 160 ASP cc_start: 0.8269 (m-30) cc_final: 0.7632 (m-30) REVERT: I 283 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7705 (ttt) REVERT: I 321 ASP cc_start: 0.8755 (p0) cc_final: 0.8408 (p0) outliers start: 37 outliers final: 25 residues processed: 233 average time/residue: 0.4482 time to fit residues: 119.2036 Evaluate side-chains 241 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 213 CYS Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.085544 restraints weight = 46398.560| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.41 r_work: 0.2806 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 17450 Z= 0.205 Angle : 0.597 13.804 23855 Z= 0.294 Chirality : 0.044 0.230 2730 Planarity : 0.004 0.054 2935 Dihedral : 4.570 64.567 2770 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.75 % Allowed : 11.58 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2045 helix: 1.55 (0.17), residues: 860 sheet: -0.94 (0.23), residues: 430 loop : -0.08 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 441 TYR 0.013 0.001 TYR C 442 PHE 0.016 0.001 PHE A 297 TRP 0.010 0.001 TRP F 11 HIS 0.005 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00500 (17405) covalent geometry : angle 0.58428 (23740) SS BOND : bond 0.00876 ( 20) SS BOND : angle 2.51546 ( 40) hydrogen bonds : bond 0.03735 ( 873) hydrogen bonds : angle 4.51077 ( 2802) link_BETA1-4 : bond 0.00088 ( 10) link_BETA1-4 : angle 0.96214 ( 30) link_NAG-ASN : bond 0.00308 ( 15) link_NAG-ASN : angle 1.66854 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 0.664 Fit side-chains REVERT: A 64 ASP cc_start: 0.8582 (t0) cc_final: 0.7995 (t0) REVERT: A 120 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: A 441 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7363 (mtm110) REVERT: B 10 ARG cc_start: 0.8380 (tmm-80) cc_final: 0.7308 (ttm-80) REVERT: G 66 ASP cc_start: 0.8132 (t0) cc_final: 0.7600 (t0) REVERT: I 64 ASP cc_start: 0.8518 (t0) cc_final: 0.8262 (t0) REVERT: I 283 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7768 (ttt) REVERT: I 321 ASP cc_start: 0.8777 (p0) cc_final: 0.8450 (p0) outliers start: 32 outliers final: 22 residues processed: 234 average time/residue: 0.4667 time to fit residues: 124.5794 Evaluate side-chains 243 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 0.0870 chunk 169 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.089732 restraints weight = 35127.523| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.98 r_work: 0.2881 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 17450 Z= 0.129 Angle : 0.554 15.051 23855 Z= 0.277 Chirality : 0.042 0.308 2730 Planarity : 0.004 0.048 2935 Dihedral : 4.394 69.901 2770 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.58 % Allowed : 11.91 % Favored : 86.50 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 2045 helix: 1.61 (0.16), residues: 890 sheet: -0.76 (0.24), residues: 425 loop : 0.02 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 441 TYR 0.009 0.001 TYR C 442 PHE 0.013 0.001 PHE A 297 TRP 0.014 0.001 TRP F 11 HIS 0.004 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00316 (17405) covalent geometry : angle 0.53437 (23740) SS BOND : bond 0.00929 ( 20) SS BOND : angle 3.25733 ( 40) hydrogen bonds : bond 0.03414 ( 873) hydrogen bonds : angle 4.35451 ( 2802) link_BETA1-4 : bond 0.00283 ( 10) link_BETA1-4 : angle 0.86480 ( 30) link_NAG-ASN : bond 0.00146 ( 15) link_NAG-ASN : angle 1.54551 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.635 Fit side-chains REVERT: A 64 ASP cc_start: 0.8531 (t0) cc_final: 0.7981 (t0) REVERT: A 120 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: A 160 ASP cc_start: 0.8101 (m-30) cc_final: 0.7326 (m-30) REVERT: A 441 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7340 (mtm110) REVERT: E 160 ASP cc_start: 0.8206 (m-30) cc_final: 0.7967 (m-30) REVERT: G 66 ASP cc_start: 0.8051 (t0) cc_final: 0.7566 (t0) REVERT: I 64 ASP cc_start: 0.8477 (t0) cc_final: 0.8212 (t0) REVERT: I 160 ASP cc_start: 0.8107 (m-30) cc_final: 0.7272 (m-30) REVERT: I 283 MET cc_start: 0.8000 (ttp) cc_final: 0.7717 (ttt) REVERT: I 321 ASP cc_start: 0.8773 (p0) cc_final: 0.8452 (p0) outliers start: 29 outliers final: 18 residues processed: 231 average time/residue: 0.4660 time to fit residues: 122.9429 Evaluate side-chains 235 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain I residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 40 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 191 optimal weight: 5.9990 chunk 119 optimal weight: 0.0980 chunk 122 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 ASN ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.089303 restraints weight = 48408.364| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.46 r_work: 0.2860 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 17450 Z= 0.127 Angle : 0.558 16.572 23855 Z= 0.277 Chirality : 0.042 0.315 2730 Planarity : 0.004 0.050 2935 Dihedral : 4.267 71.278 2770 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.26 % Allowed : 12.73 % Favored : 86.01 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2045 helix: 1.63 (0.16), residues: 890 sheet: -0.70 (0.24), residues: 425 loop : 0.04 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 441 TYR 0.011 0.001 TYR C 442 PHE 0.018 0.001 PHE A 297 TRP 0.018 0.001 TRP F 11 HIS 0.004 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00316 (17405) covalent geometry : angle 0.53613 (23740) SS BOND : bond 0.01018 ( 20) SS BOND : angle 3.39643 ( 40) hydrogen bonds : bond 0.03329 ( 873) hydrogen bonds : angle 4.28294 ( 2802) link_BETA1-4 : bond 0.00249 ( 10) link_BETA1-4 : angle 0.93313 ( 30) link_NAG-ASN : bond 0.00115 ( 15) link_NAG-ASN : angle 1.55328 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.411 Fit side-chains REVERT: A 64 ASP cc_start: 0.8581 (t0) cc_final: 0.7975 (t0) REVERT: A 120 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: A 160 ASP cc_start: 0.8092 (m-30) cc_final: 0.7205 (m-30) REVERT: A 441 ARG cc_start: 0.7738 (mtm110) cc_final: 0.7480 (mtm110) REVERT: C 452 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7286 (mt-10) REVERT: E 160 ASP cc_start: 0.8265 (m-30) cc_final: 0.7888 (m-30) REVERT: E 473 MET cc_start: 0.7010 (mtp) cc_final: 0.6257 (ptt) REVERT: G 66 ASP cc_start: 0.8048 (t0) cc_final: 0.7537 (t0) REVERT: I 64 ASP cc_start: 0.8468 (t0) cc_final: 0.8256 (t0) REVERT: I 160 ASP cc_start: 0.8193 (m-30) cc_final: 0.7448 (m-30) REVERT: I 283 MET cc_start: 0.8019 (ttp) cc_final: 0.7743 (ttt) REVERT: I 321 ASP cc_start: 0.8761 (p0) cc_final: 0.8468 (p0) outliers start: 23 outliers final: 17 residues processed: 226 average time/residue: 0.4610 time to fit residues: 118.3173 Evaluate side-chains 233 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain E residue 213 CYS Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 192 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 175 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN ** I 137 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.128649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.089325 restraints weight = 49491.022| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.52 r_work: 0.2833 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.160 17450 Z= 0.131 Angle : 0.558 17.302 23855 Z= 0.278 Chirality : 0.042 0.315 2730 Planarity : 0.004 0.049 2935 Dihedral : 4.207 71.646 2770 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.31 % Allowed : 12.57 % Favored : 86.12 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2045 helix: 1.63 (0.16), residues: 890 sheet: -0.65 (0.24), residues: 425 loop : 0.07 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 441 TYR 0.011 0.001 TYR C 442 PHE 0.018 0.001 PHE A 297 TRP 0.020 0.001 TRP F 11 HIS 0.004 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00327 (17405) covalent geometry : angle 0.53585 (23740) SS BOND : bond 0.00983 ( 20) SS BOND : angle 3.48672 ( 40) hydrogen bonds : bond 0.03317 ( 873) hydrogen bonds : angle 4.26414 ( 2802) link_BETA1-4 : bond 0.00250 ( 10) link_BETA1-4 : angle 0.92498 ( 30) link_NAG-ASN : bond 0.00111 ( 15) link_NAG-ASN : angle 1.55449 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4956.26 seconds wall clock time: 85 minutes 9.10 seconds (5109.10 seconds total)