Starting phenix.real_space_refine on Sun Dec 29 06:40:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tye_41715/12_2024/8tye_41715.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tye_41715/12_2024/8tye_41715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tye_41715/12_2024/8tye_41715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tye_41715/12_2024/8tye_41715.map" model { file = "/net/cci-nas-00/data/ceres_data/8tye_41715/12_2024/8tye_41715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tye_41715/12_2024/8tye_41715.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 90 5.16 5 C 6178 2.51 5 N 1630 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9921 Number of models: 1 Model: "" Number of chains: 33 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "C" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 2 Chain: "A" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 2 Chain: "B" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1463 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 2 Chain: "c" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1251 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "a" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1189 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain breaks: 1 Chain: "b" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1189 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain breaks: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: "C" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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 Time building chain proxies: 8.67, per 1000 atoms: 0.87 Number of scatterers: 9921 At special positions: 0 Unit cell: (104.4, 97.15, 103.675, 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 90 16.00 O 2023 8.00 N 1630 7.00 C 6178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=1.66 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.04 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG D 1 " - " FUC D 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " " NAG K 1 " - " FUC K 3 " NAG-ASN " NAG A 301 " - " ASN A 109 " " NAG A 302 " - " ASN A 89 " " NAG A 303 " - " ASN A 99 " " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 119 " " NAG C 301 " - " ASN C 89 " " NAG C 302 " - " ASN C 99 " " NAG D 1 " - " ASN C 109 " " NAG E 1 " - " ASN C 79 " " NAG F 1 " - " ASN C 119 " " NAG G 1 " - " ASN C 167 " " NAG I 1 " - " ASN C 224 " " NAG J 1 " - " ASN A 79 " " NAG K 1 " - " ASN A 119 " " NAG M 1 " - " ASN A 167 " " NAG N 1 " - " ASN A 224 " " NAG O 1 " - " ASN B 79 " " NAG P 1 " - " ASN B 109 " " NAG Q 1 " - " ASN B 167 " " NAG R 1 " - " ASN B 224 " " NAG S 1 " - " ASN c 365 " " NAG T 1 " - " ASN c 373 " " NAG U 1 " - " ASN a 365 " " NAG V 1 " - " ASN a 373 " " NAG W 1 " - " ASN b 365 " " NAG X 1 " - " ASN b 373 " " NAG a 701 " - " ASN a 395 " " NAG a 702 " - " ASN a 390 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 14 sheets defined 39.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'C' and resid 75 through 80 removed outlier: 4.345A pdb=" N MET C 80 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.987A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 4.054A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.949A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.793A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.867A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.049A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.669A pdb=" N LEU A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 removed outlier: 4.476A pdb=" N THR A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'B' and resid 74 through 81 removed outlier: 4.042A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.588A pdb=" N GLY B 160 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.943A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.061A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 301 removed outlier: 3.802A pdb=" N LYS c 300 " --> pdb=" O THR c 296 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 325 removed outlier: 3.674A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 345 removed outlier: 6.162A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.950A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 414 removed outlier: 3.590A pdb=" N ILE c 403 " --> pdb=" O PHE c 399 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR c 412 " --> pdb=" O ASP c 408 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU c 413 " --> pdb=" O ASN c 409 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET c 414 " --> pdb=" O MET c 410 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 302 removed outlier: 3.548A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN a 302 " --> pdb=" O VAL a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 308 through 326 Processing helix chain 'a' and resid 334 through 339 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.827A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 413 removed outlier: 4.039A pdb=" N GLU a 413 " --> pdb=" O ASN a 409 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 304 removed outlier: 3.577A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN b 302 " --> pdb=" O VAL b 298 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU b 303 " --> pdb=" O ALA b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 326 removed outlier: 3.822A pdb=" N GLN b 324 " --> pdb=" O LYS b 320 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU b 326 " --> pdb=" O ALA b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 340 removed outlier: 3.669A pdb=" N ALA b 340 " --> pdb=" O LEU b 336 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.533A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 396 through 398 No H-bonds generated for 'chain 'b' and resid 396 through 398' Processing helix chain 'b' and resid 399 through 414 removed outlier: 4.007A pdb=" N GLU b 413 " --> pdb=" O ASN b 409 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET b 414 " --> pdb=" O MET b 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 35A through 38 Processing sheet with id=AA2, first strand: chain 'H' and resid 65 through 68 Processing sheet with id=AA3, first strand: chain 'L' and resid 35 through 37 Processing sheet with id=AA4, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 removed outlier: 3.518A pdb=" N TYR C 66 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR c 371 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'A' and resid 66 through 72 removed outlier: 4.008A pdb=" N ASN a 365 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TRP a 386 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N SER a 367 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N LYS a 384 " --> pdb=" O SER a 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AB2, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB5, first strand: chain 'b' and resid 388 through 389 removed outlier: 3.540A pdb=" N SER b 389 " --> pdb=" O SER b 392 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 873 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: 2.45 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3035 1.34 - 1.46: 2528 1.46 - 1.59: 4387 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 10088 Sorted by residual: bond pdb=" C SER C 237 " pdb=" N PRO C 238 " ideal model delta sigma weight residual 1.331 1.354 -0.023 7.90e-03 1.60e+04 8.27e+00 bond pdb=" N TRP a 264 " pdb=" CA TRP a 264 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.21e+00 bond pdb=" N ILE b 286 " pdb=" CA ILE b 286 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.19e-02 7.06e+03 8.01e+00 bond pdb=" N ILE b 337 " pdb=" CA ILE b 337 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.95e+00 bond pdb=" N PHE b 262 " pdb=" CA PHE b 262 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.27e-02 6.20e+03 7.85e+00 ... (remaining 10083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12801 1.89 - 3.78: 728 3.78 - 5.67: 128 5.67 - 7.56: 30 7.56 - 9.45: 7 Bond angle restraints: 13694 Sorted by residual: angle pdb=" CB LYS A 63 " pdb=" CG LYS A 63 " pdb=" CD LYS A 63 " ideal model delta sigma weight residual 111.30 120.18 -8.88 2.30e+00 1.89e-01 1.49e+01 angle pdb=" CA CYS C 86 " pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " ideal model delta sigma weight residual 114.40 122.70 -8.30 2.30e+00 1.89e-01 1.30e+01 angle pdb=" N ILE b 334 " pdb=" CA ILE b 334 " pdb=" C ILE b 334 " ideal model delta sigma weight residual 113.07 108.19 4.88 1.36e+00 5.41e-01 1.29e+01 angle pdb=" N ASN a 365 " pdb=" CA ASN a 365 " pdb=" C ASN a 365 " ideal model delta sigma weight residual 113.28 109.01 4.27 1.22e+00 6.72e-01 1.22e+01 angle pdb=" N ALA b 330 " pdb=" CA ALA b 330 " pdb=" C ALA b 330 " ideal model delta sigma weight residual 111.28 107.48 3.80 1.09e+00 8.42e-01 1.22e+01 ... (remaining 13689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.26: 6360 22.26 - 44.52: 337 44.52 - 66.78: 63 66.78 - 89.04: 43 89.04 - 111.30: 22 Dihedral angle restraints: 6825 sinusoidal: 3260 harmonic: 3565 Sorted by residual: dihedral pdb=" CB CYS a 364 " pdb=" SG CYS a 364 " pdb=" SG CYS a 385 " pdb=" CB CYS a 385 " ideal model delta sinusoidal sigma weight residual -86.00 -169.64 83.64 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS b 360 " pdb=" CB CYS b 360 " ideal model delta sinusoidal sigma weight residual -86.00 -32.94 -53.06 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS c 360 " pdb=" CB CYS c 360 " ideal model delta sinusoidal sigma weight residual 93.00 130.83 -37.83 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 6822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 1695 0.148 - 0.296: 42 0.296 - 0.444: 6 0.444 - 0.592: 1 0.592 - 0.741: 2 Chirality restraints: 1746 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-02 2.50e+03 1.10e+03 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.11e+02 chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.33e+02 ... (remaining 1743 not shown) Planarity restraints: 1697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " -0.370 2.00e-02 2.50e+03 3.17e-01 1.25e+03 pdb=" C7 NAG T 2 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " -0.124 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " 0.562 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.346 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG E 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " 0.334 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG U 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " 0.113 2.00e-02 2.50e+03 ... (remaining 1694 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 838 2.74 - 3.28: 10384 3.28 - 3.82: 15616 3.82 - 4.36: 18268 4.36 - 4.90: 31112 Nonbonded interactions: 76218 Sorted by model distance: nonbonded pdb=" OG1 THR C 81 " pdb=" OD1 ASN c 319 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP b 311 " pdb=" NH2 ARG b 314 " model vdw 2.247 3.120 nonbonded pdb=" NZ LYS A 116 " pdb=" O7 NAG M 1 " model vdw 2.248 3.120 nonbonded pdb=" N GLY a 277 " pdb=" OD1 ASN a 295 " model vdw 2.253 3.120 nonbonded pdb=" NH2 ARG C 256 " pdb=" OG SER A 255 " model vdw 2.256 3.120 ... (remaining 76213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 60 through 259 or resid 301 through 302)) selection = (chain 'B' and (resid 60 through 197 or resid 207 through 259 or resid 301 throu \ gh 302)) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'X' and resid 1) } ncs_group { reference = chain 'E' selection = chain 'U' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) } ncs_group { reference = (chain 'H' and resid 15 through 109) selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = (chain 'c' and (resid 260 through 267 or resid 277 through 414 or resid 701 thro \ ugh 702)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.840 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10088 Z= 0.368 Angle : 1.017 9.447 13694 Z= 0.501 Chirality : 0.064 0.741 1746 Planarity : 0.025 0.317 1664 Dihedral : 16.149 111.296 4440 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 966 helix: -0.10 (0.27), residues: 309 sheet: -1.70 (0.40), residues: 158 loop : -0.92 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP a 386 HIS 0.014 0.002 HIS c 354 PHE 0.019 0.002 PHE a 318 TYR 0.025 0.002 TYR a 363 ARG 0.014 0.001 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 ASP cc_start: 0.8193 (t0) cc_final: 0.7895 (t0) REVERT: A 129 TYR cc_start: 0.7807 (p90) cc_final: 0.7553 (p90) REVERT: A 193 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7683 (mtp180) REVERT: A 194 MET cc_start: 0.7239 (tpp) cc_final: 0.6654 (tpp) REVERT: B 76 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7995 (mp0) REVERT: B 151 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 245 LEU cc_start: 0.9402 (mt) cc_final: 0.8993 (tt) REVERT: c 286 ILE cc_start: 0.8907 (pt) cc_final: 0.7969 (pt) REVERT: c 295 ASN cc_start: 0.8628 (t0) cc_final: 0.8226 (t0) REVERT: c 379 ARG cc_start: 0.8248 (mmp80) cc_final: 0.7884 (mmm160) REVERT: a 357 ASP cc_start: 0.8690 (t70) cc_final: 0.8330 (t0) REVERT: a 363 TYR cc_start: 0.7670 (p90) cc_final: 0.7463 (p90) REVERT: a 398 HIS cc_start: 0.7501 (m-70) cc_final: 0.7151 (m-70) REVERT: b 358 ILE cc_start: 0.9104 (tt) cc_final: 0.8876 (tt) REVERT: b 381 SER cc_start: 0.8877 (p) cc_final: 0.8624 (t) REVERT: b 400 SER cc_start: 0.8552 (p) cc_final: 0.8327 (m) REVERT: b 414 MET cc_start: 0.6937 (mpp) cc_final: 0.6639 (mpp) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2674 time to fit residues: 113.8949 Evaluate side-chains 254 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 ASN A 209 ASN c 354 HIS c 409 ASN a 335 GLN a 374 HIS b 335 GLN b 409 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10088 Z= 0.321 Angle : 0.855 10.473 13694 Z= 0.390 Chirality : 0.048 0.366 1746 Planarity : 0.004 0.044 1664 Dihedral : 12.019 83.845 2534 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.22 % Allowed : 11.43 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.27), residues: 966 helix: 0.38 (0.28), residues: 329 sheet: -1.57 (0.41), residues: 147 loop : -0.79 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 227 HIS 0.012 0.002 HIS B 93 PHE 0.023 0.002 PHE b 399 TYR 0.018 0.002 TYR B 241 ARG 0.009 0.001 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8555 (mppt) REVERT: A 129 TYR cc_start: 0.8229 (p90) cc_final: 0.7821 (p90) REVERT: B 67 GLU cc_start: 0.8291 (tp30) cc_final: 0.8026 (tp30) REVERT: B 76 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7924 (mp0) REVERT: B 245 LEU cc_start: 0.9513 (mt) cc_final: 0.9020 (tt) REVERT: B 257 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8190 (mtm-85) REVERT: c 284 MET cc_start: 0.8462 (mpp) cc_final: 0.7722 (mtm) REVERT: c 295 ASN cc_start: 0.8455 (t0) cc_final: 0.8222 (t0) REVERT: a 357 ASP cc_start: 0.8824 (t70) cc_final: 0.8566 (t0) REVERT: a 398 HIS cc_start: 0.7737 (m-70) cc_final: 0.7305 (m-70) REVERT: b 289 GLU cc_start: 0.8264 (mp0) cc_final: 0.8024 (mp0) REVERT: b 381 SER cc_start: 0.8964 (p) cc_final: 0.8471 (t) REVERT: b 400 SER cc_start: 0.8632 (p) cc_final: 0.8302 (m) outliers start: 20 outliers final: 13 residues processed: 274 average time/residue: 0.2475 time to fit residues: 92.0684 Evaluate side-chains 254 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 344 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 321 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 107 optimal weight: 0.2980 chunk 115 optimal weight: 0.0020 chunk 95 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 HIS ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS c 409 ASN a 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10088 Z= 0.188 Angle : 0.728 9.873 13694 Z= 0.337 Chirality : 0.045 0.332 1746 Planarity : 0.003 0.039 1664 Dihedral : 10.172 77.434 2534 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.22 % Allowed : 15.76 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 966 helix: 0.43 (0.28), residues: 333 sheet: -1.46 (0.40), residues: 156 loop : -0.69 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 227 HIS 0.006 0.001 HIS C 179 PHE 0.012 0.001 PHE a 399 TYR 0.022 0.001 TYR B 253 ARG 0.006 0.001 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 268 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8155 (ttp-170) REVERT: A 129 TYR cc_start: 0.8134 (p90) cc_final: 0.7786 (p90) REVERT: A 194 MET cc_start: 0.7113 (tpp) cc_final: 0.6660 (tpp) REVERT: B 67 GLU cc_start: 0.8281 (tp30) cc_final: 0.8036 (tp30) REVERT: B 76 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8022 (mp0) REVERT: B 245 LEU cc_start: 0.9502 (mt) cc_final: 0.8977 (tt) REVERT: B 257 ARG cc_start: 0.8417 (mtm180) cc_final: 0.8144 (mtm-85) REVERT: c 284 MET cc_start: 0.8460 (mpp) cc_final: 0.8028 (mtm) REVERT: c 289 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7244 (mm-30) REVERT: c 295 ASN cc_start: 0.8431 (t0) cc_final: 0.8207 (t0) REVERT: a 398 HIS cc_start: 0.7621 (m-70) cc_final: 0.7189 (m-70) REVERT: b 400 SER cc_start: 0.8620 (p) cc_final: 0.8219 (m) outliers start: 20 outliers final: 13 residues processed: 279 average time/residue: 0.2408 time to fit residues: 91.5316 Evaluate side-chains 255 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS A 179 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN b 374 HIS b 406 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10088 Z= 0.299 Angle : 0.785 10.413 13694 Z= 0.363 Chirality : 0.046 0.303 1746 Planarity : 0.004 0.038 1664 Dihedral : 9.505 80.487 2534 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.33 % Allowed : 17.54 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.27), residues: 966 helix: 0.52 (0.29), residues: 333 sheet: -1.23 (0.40), residues: 164 loop : -0.75 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 227 HIS 0.009 0.001 HIS B 93 PHE 0.016 0.002 PHE A 157 TYR 0.021 0.002 TYR B 241 ARG 0.005 0.001 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8290 (ttp-170) REVERT: A 72 GLU cc_start: 0.7967 (mp0) cc_final: 0.7692 (mp0) REVERT: A 76 GLU cc_start: 0.7966 (mp0) cc_final: 0.7568 (mp0) REVERT: A 129 TYR cc_start: 0.8123 (p90) cc_final: 0.7768 (p90) REVERT: B 67 GLU cc_start: 0.8362 (tp30) cc_final: 0.8095 (tp30) REVERT: B 76 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8011 (mp0) REVERT: B 245 LEU cc_start: 0.9493 (mt) cc_final: 0.8910 (tt) REVERT: B 257 ARG cc_start: 0.8478 (mtm180) cc_final: 0.8158 (mtm-85) REVERT: c 295 ASN cc_start: 0.8455 (t0) cc_final: 0.8222 (t0) REVERT: c 370 TRP cc_start: 0.9007 (p-90) cc_final: 0.8689 (p-90) REVERT: a 398 HIS cc_start: 0.7786 (m-70) cc_final: 0.7273 (m-70) REVERT: a 402 ASP cc_start: 0.8759 (t70) cc_final: 0.8512 (t0) REVERT: a 409 ASN cc_start: 0.8699 (m-40) cc_final: 0.8492 (m110) REVERT: a 410 MET cc_start: 0.8754 (tpp) cc_final: 0.8472 (tpp) REVERT: b 400 SER cc_start: 0.8676 (p) cc_final: 0.8260 (m) outliers start: 30 outliers final: 21 residues processed: 275 average time/residue: 0.2542 time to fit residues: 93.6990 Evaluate side-chains 265 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 374 HIS a 405 GLN b 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10088 Z= 0.233 Angle : 0.759 16.131 13694 Z= 0.349 Chirality : 0.045 0.310 1746 Planarity : 0.003 0.035 1664 Dihedral : 9.046 80.187 2534 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.77 % Allowed : 19.76 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.27), residues: 966 helix: 0.61 (0.29), residues: 331 sheet: -1.03 (0.40), residues: 162 loop : -0.80 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 210 HIS 0.005 0.001 HIS B 93 PHE 0.012 0.001 PHE a 309 TYR 0.017 0.002 TYR a 363 ARG 0.004 0.001 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 THR cc_start: 0.9266 (m) cc_final: 0.8714 (t) REVERT: C 82 MET cc_start: 0.8915 (pmm) cc_final: 0.8279 (pmm) REVERT: C 129 TYR cc_start: 0.7723 (p90) cc_final: 0.7391 (p90) REVERT: C 153 MET cc_start: 0.9334 (ppp) cc_final: 0.9077 (ppp) REVERT: A 72 GLU cc_start: 0.7971 (mp0) cc_final: 0.7672 (mp0) REVERT: A 76 GLU cc_start: 0.7961 (mp0) cc_final: 0.7552 (mp0) REVERT: A 129 TYR cc_start: 0.8039 (p90) cc_final: 0.7708 (p90) REVERT: B 67 GLU cc_start: 0.8363 (tp30) cc_final: 0.8114 (tp30) REVERT: B 76 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8016 (mp0) REVERT: B 245 LEU cc_start: 0.9504 (mt) cc_final: 0.8947 (tt) REVERT: c 284 MET cc_start: 0.9303 (mtm) cc_final: 0.9010 (mtm) REVERT: c 295 ASN cc_start: 0.8442 (t0) cc_final: 0.8235 (t0) REVERT: c 379 ARG cc_start: 0.8236 (mmp80) cc_final: 0.7991 (mmm160) REVERT: a 358 ILE cc_start: 0.9038 (mm) cc_final: 0.8816 (mm) REVERT: a 398 HIS cc_start: 0.7711 (m-70) cc_final: 0.7203 (m-70) REVERT: a 402 ASP cc_start: 0.8715 (t70) cc_final: 0.8474 (t0) REVERT: b 400 SER cc_start: 0.8675 (p) cc_final: 0.8250 (m) outliers start: 25 outliers final: 19 residues processed: 271 average time/residue: 0.2603 time to fit residues: 94.6062 Evaluate side-chains 266 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 380 THR Chi-restraints excluded: chain b residue 412 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 338 ASN a 405 GLN a 409 ASN ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10088 Z= 0.218 Angle : 0.762 14.595 13694 Z= 0.354 Chirality : 0.045 0.313 1746 Planarity : 0.003 0.031 1664 Dihedral : 8.845 79.833 2534 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.66 % Allowed : 20.42 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.27), residues: 966 helix: 0.69 (0.29), residues: 331 sheet: -1.21 (0.43), residues: 140 loop : -0.77 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 227 HIS 0.005 0.001 HIS C 141 PHE 0.015 0.001 PHE A 233 TYR 0.026 0.001 TYR B 253 ARG 0.006 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6883 (tm-30) REVERT: C 75 MET cc_start: 0.8594 (mmm) cc_final: 0.7993 (mmt) REVERT: C 82 MET cc_start: 0.8932 (pmm) cc_final: 0.8567 (pmm) REVERT: C 129 TYR cc_start: 0.7661 (p90) cc_final: 0.7355 (p90) REVERT: C 153 MET cc_start: 0.9330 (ppp) cc_final: 0.9079 (ppp) REVERT: C 250 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8310 (ttp-170) REVERT: A 72 GLU cc_start: 0.7906 (mp0) cc_final: 0.7641 (mp0) REVERT: A 76 GLU cc_start: 0.7972 (mp0) cc_final: 0.7547 (mp0) REVERT: A 129 TYR cc_start: 0.8012 (p90) cc_final: 0.7731 (p90) REVERT: A 196 TRP cc_start: 0.7730 (OUTLIER) cc_final: 0.6922 (t60) REVERT: B 67 GLU cc_start: 0.8352 (tp30) cc_final: 0.8100 (tp30) REVERT: B 76 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8060 (mp0) REVERT: B 245 LEU cc_start: 0.9481 (mt) cc_final: 0.8934 (tt) REVERT: c 295 ASN cc_start: 0.8430 (t0) cc_final: 0.8224 (t0) REVERT: c 348 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8438 (mm-40) REVERT: a 358 ILE cc_start: 0.9043 (mm) cc_final: 0.8835 (mm) REVERT: a 379 ARG cc_start: 0.7322 (ttp-170) cc_final: 0.6977 (ttp-170) REVERT: a 398 HIS cc_start: 0.7707 (m-70) cc_final: 0.7122 (m-70) REVERT: a 402 ASP cc_start: 0.8696 (t70) cc_final: 0.8468 (t0) REVERT: b 400 SER cc_start: 0.8676 (p) cc_final: 0.8222 (m) outliers start: 24 outliers final: 18 residues processed: 283 average time/residue: 0.2631 time to fit residues: 100.2487 Evaluate side-chains 271 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.0970 chunk 12 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS B 146 ASN a 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10088 Z= 0.203 Angle : 0.751 13.248 13694 Z= 0.348 Chirality : 0.044 0.316 1746 Planarity : 0.003 0.034 1664 Dihedral : 8.672 79.676 2534 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.44 % Allowed : 20.20 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.27), residues: 966 helix: 0.87 (0.30), residues: 317 sheet: -0.98 (0.43), residues: 144 loop : -0.81 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 210 HIS 0.004 0.001 HIS C 141 PHE 0.012 0.001 PHE C 191 TYR 0.019 0.001 TYR A 150 ARG 0.008 0.001 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6902 (tm-30) REVERT: C 74 ASN cc_start: 0.8427 (t0) cc_final: 0.8226 (t0) REVERT: C 81 THR cc_start: 0.9243 (m) cc_final: 0.8683 (t) REVERT: C 82 MET cc_start: 0.8956 (pmm) cc_final: 0.8276 (pmm) REVERT: C 129 TYR cc_start: 0.7642 (p90) cc_final: 0.7345 (p90) REVERT: C 153 MET cc_start: 0.9346 (ppp) cc_final: 0.9085 (ppp) REVERT: A 72 GLU cc_start: 0.7959 (mp0) cc_final: 0.7715 (mp0) REVERT: A 76 GLU cc_start: 0.7966 (mp0) cc_final: 0.7557 (mp0) REVERT: A 129 TYR cc_start: 0.8007 (p90) cc_final: 0.7693 (p90) REVERT: A 196 TRP cc_start: 0.7745 (OUTLIER) cc_final: 0.6901 (t60) REVERT: A 248 ARG cc_start: 0.9039 (ptm160) cc_final: 0.8689 (ptm160) REVERT: B 67 GLU cc_start: 0.8374 (tp30) cc_final: 0.8141 (tp30) REVERT: B 76 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8072 (mp0) REVERT: B 245 LEU cc_start: 0.9429 (mt) cc_final: 0.8952 (tt) REVERT: c 351 MET cc_start: 0.9172 (tpp) cc_final: 0.8778 (tpp) REVERT: c 379 ARG cc_start: 0.8205 (mmp80) cc_final: 0.7950 (mmm160) REVERT: a 325 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.8026 (mtt-85) REVERT: a 356 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8746 (ttp-170) REVERT: a 379 ARG cc_start: 0.7349 (ttp-170) cc_final: 0.7025 (ttp-170) REVERT: a 398 HIS cc_start: 0.7654 (m-70) cc_final: 0.7056 (m-70) REVERT: a 402 ASP cc_start: 0.8694 (t70) cc_final: 0.8470 (t0) REVERT: b 291 LYS cc_start: 0.7232 (mmtm) cc_final: 0.6961 (mmtt) REVERT: b 400 SER cc_start: 0.8658 (p) cc_final: 0.8218 (m) REVERT: b 405 GLN cc_start: 0.8766 (pm20) cc_final: 0.8448 (pm20) outliers start: 31 outliers final: 19 residues processed: 283 average time/residue: 0.2491 time to fit residues: 95.3437 Evaluate side-chains 269 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 315 LEU Chi-restraints excluded: chain a residue 356 ARG Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 364 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 0.0030 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 295 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN a 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10088 Z= 0.249 Angle : 0.774 12.967 13694 Z= 0.360 Chirality : 0.045 0.300 1746 Planarity : 0.003 0.035 1664 Dihedral : 8.647 80.625 2534 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.00 % Allowed : 21.75 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.27), residues: 966 helix: 0.81 (0.30), residues: 317 sheet: -1.00 (0.44), residues: 140 loop : -0.79 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 210 HIS 0.006 0.001 HIS B 93 PHE 0.021 0.002 PHE A 157 TYR 0.024 0.001 TYR B 241 ARG 0.011 0.001 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6856 (tm-30) REVERT: C 74 ASN cc_start: 0.8422 (t0) cc_final: 0.8221 (t0) REVERT: C 82 MET cc_start: 0.8918 (pmm) cc_final: 0.8485 (pmm) REVERT: C 129 TYR cc_start: 0.7693 (p90) cc_final: 0.7361 (p90) REVERT: C 153 MET cc_start: 0.9347 (ppp) cc_final: 0.9059 (ppp) REVERT: C 250 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8204 (ttp-170) REVERT: A 72 GLU cc_start: 0.7997 (mp0) cc_final: 0.7732 (mp0) REVERT: A 76 GLU cc_start: 0.7952 (mp0) cc_final: 0.7582 (mp0) REVERT: A 129 TYR cc_start: 0.8031 (p90) cc_final: 0.7742 (p90) REVERT: A 196 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.6910 (t60) REVERT: A 248 ARG cc_start: 0.9050 (ptm160) cc_final: 0.8722 (ptm160) REVERT: B 67 GLU cc_start: 0.8385 (tp30) cc_final: 0.8136 (tp30) REVERT: B 76 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8064 (mp0) REVERT: B 245 LEU cc_start: 0.9476 (mt) cc_final: 0.9007 (tt) REVERT: c 348 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8507 (mm-40) REVERT: c 351 MET cc_start: 0.9210 (tpp) cc_final: 0.8810 (tpp) REVERT: c 370 TRP cc_start: 0.8975 (p-90) cc_final: 0.8734 (p90) REVERT: c 379 ARG cc_start: 0.8233 (mmp80) cc_final: 0.7978 (mmm160) REVERT: a 325 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.8036 (mtt-85) REVERT: a 356 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8751 (ttp-170) REVERT: a 379 ARG cc_start: 0.7388 (ttp-170) cc_final: 0.7140 (ttp-170) REVERT: a 398 HIS cc_start: 0.7678 (m-70) cc_final: 0.7017 (m-70) REVERT: a 402 ASP cc_start: 0.8717 (t70) cc_final: 0.8489 (t0) REVERT: b 400 SER cc_start: 0.8661 (p) cc_final: 0.8242 (m) REVERT: b 405 GLN cc_start: 0.8722 (pm20) cc_final: 0.8457 (pm20) outliers start: 27 outliers final: 22 residues processed: 270 average time/residue: 0.2789 time to fit residues: 102.2204 Evaluate side-chains 270 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 344 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 356 ARG Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 364 CYS Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.0670 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 95 optimal weight: 0.0170 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN a 409 ASN b 319 ASN b 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10088 Z= 0.191 Angle : 0.759 12.168 13694 Z= 0.351 Chirality : 0.044 0.314 1746 Planarity : 0.003 0.039 1664 Dihedral : 8.410 79.183 2534 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.11 % Allowed : 22.20 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.27), residues: 966 helix: 0.83 (0.30), residues: 319 sheet: -0.81 (0.41), residues: 158 loop : -0.76 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 210 HIS 0.004 0.001 HIS c 354 PHE 0.019 0.001 PHE A 157 TYR 0.019 0.001 TYR A 150 ARG 0.009 0.001 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ASN cc_start: 0.8281 (t0) cc_final: 0.8072 (t0) REVERT: C 81 THR cc_start: 0.9223 (m) cc_final: 0.8681 (t) REVERT: C 82 MET cc_start: 0.8928 (pmm) cc_final: 0.8264 (pmm) REVERT: C 129 TYR cc_start: 0.7564 (p90) cc_final: 0.7260 (p90) REVERT: C 153 MET cc_start: 0.9294 (ppp) cc_final: 0.9049 (ppp) REVERT: C 193 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7406 (ttp80) REVERT: C 216 SER cc_start: 0.8720 (m) cc_final: 0.8388 (p) REVERT: C 250 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8191 (mmm-85) REVERT: A 76 GLU cc_start: 0.7927 (mp0) cc_final: 0.7559 (mp0) REVERT: A 129 TYR cc_start: 0.7912 (p90) cc_final: 0.7689 (p90) REVERT: A 196 TRP cc_start: 0.7700 (OUTLIER) cc_final: 0.6806 (t60) REVERT: A 248 ARG cc_start: 0.8991 (ptm160) cc_final: 0.8269 (ttm170) REVERT: B 67 GLU cc_start: 0.8408 (tp30) cc_final: 0.8172 (tp30) REVERT: B 74 ASN cc_start: 0.8281 (t0) cc_final: 0.7655 (t0) REVERT: B 76 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8052 (mt-10) REVERT: B 245 LEU cc_start: 0.9422 (mt) cc_final: 0.8925 (tt) REVERT: c 348 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8398 (mm-40) REVERT: c 351 MET cc_start: 0.9216 (tpp) cc_final: 0.8805 (tpp) REVERT: c 370 TRP cc_start: 0.8926 (p-90) cc_final: 0.8694 (p90) REVERT: c 379 ARG cc_start: 0.8165 (mmp80) cc_final: 0.7929 (mmm160) REVERT: a 398 HIS cc_start: 0.7506 (m-70) cc_final: 0.6877 (m-70) REVERT: a 402 ASP cc_start: 0.8686 (t70) cc_final: 0.8446 (t0) REVERT: b 362 PRO cc_start: 0.8690 (Cg_exo) cc_final: 0.8408 (Cg_endo) REVERT: b 368 LYS cc_start: 0.8206 (tttm) cc_final: 0.7845 (tttm) REVERT: b 400 SER cc_start: 0.8629 (p) cc_final: 0.8202 (m) REVERT: b 405 GLN cc_start: 0.8688 (pm20) cc_final: 0.8449 (pm20) outliers start: 19 outliers final: 14 residues processed: 275 average time/residue: 0.2529 time to fit residues: 93.4943 Evaluate side-chains 262 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain b residue 364 CYS Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 117 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 295 ASN a 319 ASN a 405 GLN a 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10088 Z= 0.215 Angle : 0.780 11.522 13694 Z= 0.363 Chirality : 0.044 0.311 1746 Planarity : 0.003 0.040 1664 Dihedral : 8.346 79.413 2534 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.22 % Allowed : 23.42 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.27), residues: 966 helix: 0.85 (0.30), residues: 319 sheet: -0.76 (0.41), residues: 160 loop : -0.79 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 210 HIS 0.006 0.001 HIS B 93 PHE 0.018 0.002 PHE c 309 TYR 0.022 0.001 TYR B 241 ARG 0.009 0.001 ARG A 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ASN cc_start: 0.8230 (t0) cc_final: 0.7962 (t0) REVERT: C 81 THR cc_start: 0.9260 (m) cc_final: 0.8687 (t) REVERT: C 82 MET cc_start: 0.8929 (pmm) cc_final: 0.8237 (pmm) REVERT: C 129 TYR cc_start: 0.7533 (p90) cc_final: 0.7257 (p90) REVERT: C 153 MET cc_start: 0.9295 (ppp) cc_final: 0.9000 (ppp) REVERT: C 193 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7577 (ttp80) REVERT: C 250 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7928 (ttp-170) REVERT: A 76 GLU cc_start: 0.7922 (mp0) cc_final: 0.7567 (mp0) REVERT: A 129 TYR cc_start: 0.7936 (p90) cc_final: 0.7691 (p90) REVERT: A 196 TRP cc_start: 0.7722 (OUTLIER) cc_final: 0.6794 (t60) REVERT: A 248 ARG cc_start: 0.8969 (ptm160) cc_final: 0.8260 (ttm170) REVERT: B 67 GLU cc_start: 0.8410 (tp30) cc_final: 0.8176 (tp30) REVERT: B 76 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 245 LEU cc_start: 0.9392 (mt) cc_final: 0.8934 (tt) REVERT: c 348 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8425 (mm-40) REVERT: c 351 MET cc_start: 0.9216 (tpp) cc_final: 0.8821 (tpp) REVERT: c 370 TRP cc_start: 0.8937 (p-90) cc_final: 0.8704 (p90) REVERT: a 321 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8733 (mm-40) REVERT: a 398 HIS cc_start: 0.7481 (m-70) cc_final: 0.6839 (m-70) REVERT: a 402 ASP cc_start: 0.8689 (t70) cc_final: 0.8453 (t0) REVERT: b 308 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: b 362 PRO cc_start: 0.8703 (Cg_exo) cc_final: 0.8460 (Cg_endo) REVERT: b 368 LYS cc_start: 0.8315 (tttm) cc_final: 0.8055 (tttm) REVERT: b 400 SER cc_start: 0.8628 (p) cc_final: 0.8217 (m) REVERT: b 405 GLN cc_start: 0.8673 (pm20) cc_final: 0.8457 (pm20) outliers start: 20 outliers final: 15 residues processed: 275 average time/residue: 0.2473 time to fit residues: 92.1052 Evaluate side-chains 268 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 308 GLU Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 364 CYS Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN c 295 ASN ** a 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 GLN b 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.122958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.102462 restraints weight = 21167.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.105643 restraints weight = 11747.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107897 restraints weight = 7790.512| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10088 Z= 0.327 Angle : 0.845 12.583 13694 Z= 0.394 Chirality : 0.046 0.295 1746 Planarity : 0.004 0.036 1664 Dihedral : 8.715 82.531 2534 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.00 % Allowed : 23.53 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.27), residues: 966 helix: 0.75 (0.30), residues: 320 sheet: -1.02 (0.43), residues: 146 loop : -0.87 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 210 HIS 0.009 0.001 HIS B 93 PHE 0.024 0.002 PHE C 140 TYR 0.030 0.002 TYR B 241 ARG 0.009 0.001 ARG A 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2694.27 seconds wall clock time: 51 minutes 12.12 seconds (3072.12 seconds total)