Starting phenix.real_space_refine on Tue Jul 29 08:51:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eji_28183/07_2025/8eji_28183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eji_28183/07_2025/8eji_28183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eji_28183/07_2025/8eji_28183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eji_28183/07_2025/8eji_28183.map" model { file = "/net/cci-nas-00/data/ceres_data/8eji_28183/07_2025/8eji_28183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eji_28183/07_2025/8eji_28183.cif" } resolution = 3.81 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= 0.003 sd= 0.032 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 97 5.16 5 C 6886 2.51 5 N 1742 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11023 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "a" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1286 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "B" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1504 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain breaks: 1 Chain: "b" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1223 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain breaks: 1 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1504 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain breaks: 1 Chain: "c" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1232 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "D" 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: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" 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: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" 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: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" 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: "O" 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "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 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "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 Time building chain proxies: 7.24, per 1000 atoms: 0.66 Number of scatterers: 11023 At special positions: 0 Unit cell: (125.4, 96.14, 107.635, 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 97 16.00 O 2298 8.00 N 1742 7.00 C 6886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.08 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.08 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " MAN E 4 " - " MAN E 5 " " BMA G 3 " - " MAN G 5 " " BMA M 3 " - " MAN M 5 " " BMA R 3 " - " MAN R 6 " " BMA W 3 " - " MAN W 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 109 " " NAG B 304 " - " ASN B 119 " " NAG C 301 " - " ASN C 89 " " NAG C 302 " - " ASN C 99 " " NAG C 303 " - " ASN C 109 " " NAG C 304 " - " ASN C 119 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 99 " " NAG G 1 " - " ASN A 109 " " NAG I 1 " - " ASN A 119 " " NAG J 1 " - " ASN A 167 " " NAG K 1 " - " ASN A 224 " " NAG M 1 " - " ASN a 365 " " NAG N 1 " - " ASN a 373 " " NAG O 1 " - " ASN B 79 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN B 224 " " NAG R 1 " - " ASN b 365 " " NAG S 1 " - " ASN b 373 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 167 " " NAG V 1 " - " ASN C 224 " " NAG W 1 " - " ASN c 365 " " NAG X 1 " - " ASN c 373 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " 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: 3.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2362 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 37.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.946A pdb=" N ILE A 213 " --> pdb=" O TRP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.603A pdb=" N LEU A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 304 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 329 through 333 removed outlier: 3.541A pdb=" N SER a 333 " --> pdb=" O ALA a 330 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 339 Processing helix chain 'a' and resid 340 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.587A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 418 removed outlier: 5.603A pdb=" N ASP a 401 " --> pdb=" O THR a 397 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASP a 402 " --> pdb=" O HIS a 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.544A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 195 through 203 removed outlier: 4.384A pdb=" N TYR B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.819A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 302 removed outlier: 3.559A pdb=" N ASN b 302 " --> pdb=" O VAL b 298 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 333 through 345 removed outlier: 3.894A pdb=" N LYS b 339 " --> pdb=" O GLN b 335 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.603A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 417 Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 96 through 100 Processing helix chain 'L' and resid 95 through 99 removed outlier: 4.017A pdb=" N PHE L 99 " --> pdb=" O PRO L 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.543A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 195 through 203 removed outlier: 4.385A pdb=" N TYR C 200 " --> pdb=" O TRP C 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.818A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 302 removed outlier: 3.559A pdb=" N ASN c 302 " --> pdb=" O VAL c 298 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 333 through 345 removed outlier: 3.895A pdb=" N LYS c 339 " --> pdb=" O GLN c 335 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.604A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.628A pdb=" N GLY A 102 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 279 through 281 Processing sheet with id=AA4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 72 removed outlier: 9.249A pdb=" N TYR b 366 " --> pdb=" O VAL b 388 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N VAL b 388 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS b 368 " --> pdb=" O TRP b 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AA8, first strand: chain 'b' and resid 278 through 280 removed outlier: 3.635A pdb=" N LYS b 291 " --> pdb=" O LEU b 280 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.923A pdb=" N MET H 39 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.563A pdb=" N LEU L 11 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU L 39 " --> pdb=" O ASN L 55 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.563A pdb=" N LEU L 11 " --> pdb=" O ASP L 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB7, first strand: chain 'C' and resid 71 through 72 removed outlier: 9.249A pdb=" N TYR c 366 " --> pdb=" O VAL c 388 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N VAL c 388 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS c 368 " --> pdb=" O TRP c 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AB9, first strand: chain 'c' and resid 278 through 280 removed outlier: 3.635A pdb=" N LYS c 291 " --> pdb=" O LEU c 280 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2105 1.32 - 1.45: 3702 1.45 - 1.59: 5255 1.59 - 1.72: 36 1.72 - 1.86: 146 Bond restraints: 11244 Sorted by residual: bond pdb=" CB HIS A 170 " pdb=" CG HIS A 170 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.16e+01 bond pdb=" CB HIS A 93 " pdb=" CG HIS A 93 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" CB HIS a 354 " pdb=" CG HIS a 354 " ideal model delta sigma weight residual 1.497 1.414 0.083 1.40e-02 5.10e+03 3.55e+01 bond pdb=" CB LEU a 372 " pdb=" CG LEU a 372 " ideal model delta sigma weight residual 1.530 1.422 0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" CB HIS H 40 " pdb=" CG HIS H 40 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.76e+01 ... (remaining 11239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 13396 2.73 - 5.47: 1597 5.47 - 8.20: 200 8.20 - 10.93: 27 10.93 - 13.66: 6 Bond angle restraints: 15226 Sorted by residual: angle pdb=" N LEU a 382 " pdb=" CA LEU a 382 " pdb=" C LEU a 382 " ideal model delta sigma weight residual 109.83 99.24 10.59 1.27e+00 6.20e-01 6.96e+01 angle pdb=" C SER a 267 " pdb=" CA SER a 267 " pdb=" CB SER a 267 " ideal model delta sigma weight residual 117.23 107.05 10.18 1.36e+00 5.41e-01 5.61e+01 angle pdb=" C TRP c 370 " pdb=" CA TRP c 370 " pdb=" CB TRP c 370 " ideal model delta sigma weight residual 110.85 98.41 12.44 1.70e+00 3.46e-01 5.36e+01 angle pdb=" C TRP b 370 " pdb=" CA TRP b 370 " pdb=" CB TRP b 370 " ideal model delta sigma weight residual 110.85 98.45 12.40 1.70e+00 3.46e-01 5.32e+01 angle pdb=" N LEU c 382 " pdb=" CA LEU c 382 " pdb=" C LEU c 382 " ideal model delta sigma weight residual 109.50 99.00 10.50 1.47e+00 4.63e-01 5.10e+01 ... (remaining 15221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 7300 21.72 - 43.44: 225 43.44 - 65.16: 43 65.16 - 86.88: 75 86.88 - 108.60: 54 Dihedral angle restraints: 7697 sinusoidal: 4029 harmonic: 3668 Sorted by residual: dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 105 " pdb=" CB CYS H 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.90 -73.90 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual -86.00 -158.57 72.57 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 231 " pdb=" CB CYS B 231 " ideal model delta sinusoidal sigma weight residual -86.00 -158.53 72.53 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 7694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1292 0.119 - 0.239: 409 0.239 - 0.358: 146 0.358 - 0.478: 62 0.478 - 0.597: 9 Chirality restraints: 1918 Sorted by residual: chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-02 2.50e+03 6.36e+02 chirality pdb=" C1 BMA W 3 " pdb=" O4 NAG W 2 " pdb=" C2 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.47e+02 chirality pdb=" C1 MAN W 5 " pdb=" O2 MAN W 4 " pdb=" C2 MAN W 5 " pdb=" O5 MAN W 5 " both_signs ideal model delta sigma weight residual False 2.40 2.75 -0.35 2.00e-02 2.50e+03 3.00e+02 ... (remaining 1915 not shown) Planarity restraints: 1836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG S 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 2 " 0.355 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG X 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG X 2 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG X 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG X 2 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.349 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG R 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.179 2.00e-02 2.50e+03 ... (remaining 1833 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3323 2.83 - 3.35: 10668 3.35 - 3.86: 18681 3.86 - 4.38: 22634 4.38 - 4.90: 35563 Nonbonded interactions: 90869 Sorted by model distance: nonbonded pdb=" O4 MAN J 4 " pdb=" O6 MAN J 4 " model vdw 2.309 3.040 nonbonded pdb=" NZ LYS a 339 " pdb=" OD2 ASP B 251 " model vdw 2.409 3.120 nonbonded pdb=" OD2 ASP H 82 " pdb=" NZ LYS H 85 " model vdw 2.410 3.120 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.419 3.040 nonbonded pdb=" N ASP c 306 " pdb=" OD1 ASP c 306 " model vdw 2.419 3.120 ... (remaining 90864 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 59 through 171 or resid 179 through 255)) selection = (chain 'B' and resid 59 through 255) selection = (chain 'C' and resid 59 through 255) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'R' selection = chain 'W' } ncs_group { reference = (chain 'a' and (resid 260 through 268 or resid 277 through 417 or resid 701 thro \ ugh 702)) selection = chain 'b' selection = (chain 'c' and (resid 260 through 417 or resid 701 through 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=1.00 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: 0.010 Normalize map: mean=0, sd=1: 11.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.990 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.023 0.134 11345 Z= 1.213 Angle : 1.907 13.663 15506 Z= 1.172 Chirality : 0.148 0.597 1918 Planarity : 0.018 0.306 1803 Dihedral : 16.973 108.601 5266 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1231 helix: -0.12 (0.25), residues: 358 sheet: 0.71 (0.33), residues: 232 loop : 0.27 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.009 TRP A 196 HIS 0.015 0.003 HIS c 374 PHE 0.034 0.006 PHE L 118 TYR 0.056 0.009 TYR a 363 ARG 0.005 0.001 ARG C 248 Details of bonding type rmsd link_NAG-ASN : bond 0.06888 ( 33) link_NAG-ASN : angle 3.47607 ( 99) link_ALPHA1-6 : bond 0.05289 ( 5) link_ALPHA1-6 : angle 2.76301 ( 15) link_BETA1-4 : bond 0.06286 ( 31) link_BETA1-4 : angle 4.77463 ( 93) link_ALPHA1-2 : bond 0.00488 ( 2) link_ALPHA1-2 : angle 5.91152 ( 6) link_ALPHA1-3 : bond 0.06881 ( 7) link_ALPHA1-3 : angle 4.50911 ( 21) hydrogen bonds : bond 0.17826 ( 447) hydrogen bonds : angle 7.33024 ( 1185) SS BOND : bond 0.01612 ( 23) SS BOND : angle 2.62679 ( 46) covalent geometry : bond 0.02204 (11244) covalent geometry : angle 1.84806 (15226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9141 (ptp) cc_final: 0.8918 (ptp) REVERT: A 134 MET cc_start: 0.9087 (tpp) cc_final: 0.8266 (tpp) REVERT: a 284 MET cc_start: 0.9002 (mtp) cc_final: 0.8580 (mtt) REVERT: a 347 ASP cc_start: 0.8227 (p0) cc_final: 0.7863 (p0) REVERT: a 405 GLN cc_start: 0.8905 (tp40) cc_final: 0.8532 (tp-100) REVERT: a 408 ASP cc_start: 0.8508 (m-30) cc_final: 0.8101 (t70) REVERT: b 289 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7130 (pm20) REVERT: b 312 MET cc_start: 0.8916 (mmm) cc_final: 0.8691 (mmm) REVERT: H 39 MET cc_start: 0.8371 (mmm) cc_final: 0.8029 (mmt) REVERT: H 126 VAL cc_start: 0.9228 (t) cc_final: 0.9008 (p) REVERT: L 98 ASP cc_start: 0.8550 (m-30) cc_final: 0.8193 (m-30) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2650 time to fit residues: 118.8062 Evaluate side-chains 146 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 170 HIS A 179 HIS A 247 GLN a 305 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** b 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065345 restraints weight = 35869.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.067977 restraints weight = 19203.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.069779 restraints weight = 12902.262| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11345 Z= 0.198 Angle : 1.015 16.302 15506 Z= 0.467 Chirality : 0.053 0.340 1918 Planarity : 0.004 0.033 1803 Dihedral : 14.461 89.599 2929 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.18 % Rotamer: Outliers : 2.22 % Allowed : 9.96 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1231 helix: 0.58 (0.26), residues: 370 sheet: 1.05 (0.36), residues: 198 loop : -0.49 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP c 370 HIS 0.008 0.001 HIS A 115 PHE 0.022 0.002 PHE C 117 TYR 0.017 0.002 TYR A 66 ARG 0.006 0.001 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00915 ( 33) link_NAG-ASN : angle 4.62019 ( 99) link_ALPHA1-6 : bond 0.00691 ( 5) link_ALPHA1-6 : angle 1.78221 ( 15) link_BETA1-4 : bond 0.00866 ( 31) link_BETA1-4 : angle 3.94518 ( 93) link_ALPHA1-2 : bond 0.00296 ( 2) link_ALPHA1-2 : angle 2.35912 ( 6) link_ALPHA1-3 : bond 0.01029 ( 7) link_ALPHA1-3 : angle 2.93939 ( 21) hydrogen bonds : bond 0.05607 ( 447) hydrogen bonds : angle 5.47835 ( 1185) SS BOND : bond 0.00416 ( 23) SS BOND : angle 1.66258 ( 46) covalent geometry : bond 0.00416 (11244) covalent geometry : angle 0.88917 (15226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9215 (tpp) cc_final: 0.7608 (tpp) REVERT: A 150 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: A 192 MET cc_start: 0.8885 (tpp) cc_final: 0.8676 (tpp) REVERT: A 194 MET cc_start: 0.9062 (tpp) cc_final: 0.8767 (tpp) REVERT: A 210 TRP cc_start: 0.7124 (t60) cc_final: 0.6797 (t60) REVERT: a 278 TYR cc_start: 0.6977 (t80) cc_final: 0.6718 (t80) REVERT: a 284 MET cc_start: 0.8703 (mtp) cc_final: 0.8140 (mtt) REVERT: a 311 ASP cc_start: 0.9125 (m-30) cc_final: 0.8730 (t70) REVERT: a 332 MET cc_start: 0.8568 (tmm) cc_final: 0.7883 (tmm) REVERT: a 347 ASP cc_start: 0.8269 (p0) cc_final: 0.7560 (p0) REVERT: a 405 GLN cc_start: 0.8929 (tp40) cc_final: 0.8515 (tp40) REVERT: a 408 ASP cc_start: 0.8528 (m-30) cc_final: 0.8088 (t70) REVERT: B 140 PHE cc_start: 0.8632 (t80) cc_final: 0.8411 (t80) REVERT: B 189 GLN cc_start: 0.8790 (mt0) cc_final: 0.8457 (tt0) REVERT: B 192 MET cc_start: 0.8362 (tpt) cc_final: 0.8129 (tpp) REVERT: B 214 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6945 (pmm) REVERT: b 289 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7406 (mm-30) REVERT: b 347 ASP cc_start: 0.7952 (p0) cc_final: 0.7404 (p0) REVERT: H 96 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.8038 (mmm-85) REVERT: L 98 ASP cc_start: 0.8493 (m-30) cc_final: 0.8054 (m-30) REVERT: L 106 GLN cc_start: 0.7628 (pp30) cc_final: 0.6968 (pp30) REVERT: c 312 MET cc_start: 0.8793 (mmm) cc_final: 0.8103 (mmm) REVERT: c 370 TRP cc_start: 0.7667 (m-10) cc_final: 0.7053 (m-10) outliers start: 25 outliers final: 11 residues processed: 205 average time/residue: 0.2546 time to fit residues: 75.3621 Evaluate side-chains 159 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 150 TYR Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 345 ILE Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 chunk 107 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN a 305 HIS ** a 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS b 348 GLN L 43 GLN C 93 HIS C 114 ASN C 146 ASN C 185 ASN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.078548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.063704 restraints weight = 37253.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.066373 restraints weight = 19726.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068188 restraints weight = 13272.489| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11345 Z= 0.161 Angle : 0.866 13.253 15506 Z= 0.394 Chirality : 0.048 0.307 1918 Planarity : 0.004 0.041 1803 Dihedral : 11.402 78.998 2929 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.76 % Allowed : 11.38 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.05 (0.23), residues: 1231 helix: 0.77 (0.27), residues: 373 sheet: 1.00 (0.34), residues: 221 loop : -0.75 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 227 HIS 0.018 0.002 HIS A 179 PHE 0.024 0.002 PHE c 399 TYR 0.020 0.002 TYR A 62 ARG 0.010 0.001 ARG b 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 33) link_NAG-ASN : angle 3.98131 ( 99) link_ALPHA1-6 : bond 0.00719 ( 5) link_ALPHA1-6 : angle 1.79288 ( 15) link_BETA1-4 : bond 0.00710 ( 31) link_BETA1-4 : angle 3.04866 ( 93) link_ALPHA1-2 : bond 0.00332 ( 2) link_ALPHA1-2 : angle 2.36395 ( 6) link_ALPHA1-3 : bond 0.01173 ( 7) link_ALPHA1-3 : angle 2.56209 ( 21) hydrogen bonds : bond 0.04499 ( 447) hydrogen bonds : angle 5.11288 ( 1185) SS BOND : bond 0.00369 ( 23) SS BOND : angle 1.34604 ( 46) covalent geometry : bond 0.00339 (11244) covalent geometry : angle 0.76369 (15226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9196 (tpp) cc_final: 0.7669 (tpp) REVERT: a 284 MET cc_start: 0.8724 (mtp) cc_final: 0.8222 (mtt) REVERT: a 311 ASP cc_start: 0.9171 (m-30) cc_final: 0.8831 (t70) REVERT: a 332 MET cc_start: 0.8930 (tmm) cc_final: 0.7606 (tmm) REVERT: a 347 ASP cc_start: 0.8263 (p0) cc_final: 0.7780 (p0) REVERT: a 353 ASN cc_start: 0.9018 (m-40) cc_final: 0.8780 (m-40) REVERT: a 382 LEU cc_start: 0.9150 (tt) cc_final: 0.8783 (tt) REVERT: a 408 ASP cc_start: 0.8435 (m-30) cc_final: 0.8057 (t70) REVERT: B 134 MET cc_start: 0.8596 (tpp) cc_final: 0.8277 (tpp) REVERT: B 192 MET cc_start: 0.8216 (tpt) cc_final: 0.7915 (tpp) REVERT: b 347 ASP cc_start: 0.7848 (p0) cc_final: 0.7596 (p0) REVERT: L 87 PHE cc_start: 0.8197 (m-80) cc_final: 0.7698 (m-10) REVERT: L 89 LEU cc_start: 0.8505 (tp) cc_final: 0.8292 (tp) REVERT: L 98 ASP cc_start: 0.8413 (m-30) cc_final: 0.7932 (m-30) REVERT: L 106 GLN cc_start: 0.7703 (pp30) cc_final: 0.7275 (pp30) REVERT: c 361 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8566 (tt) outliers start: 31 outliers final: 17 residues processed: 181 average time/residue: 0.2319 time to fit residues: 59.5952 Evaluate side-chains 162 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 345 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 77 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 247 GLN a 305 HIS a 405 GLN B 185 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.077497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063181 restraints weight = 36658.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065699 restraints weight = 19740.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067455 restraints weight = 13402.858| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11345 Z= 0.152 Angle : 0.813 13.100 15506 Z= 0.370 Chirality : 0.046 0.311 1918 Planarity : 0.004 0.044 1803 Dihedral : 10.000 70.802 2929 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.49 % Allowed : 12.44 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.03 (0.23), residues: 1231 helix: 0.88 (0.27), residues: 375 sheet: 0.83 (0.34), residues: 234 loop : -0.83 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 283 HIS 0.011 0.001 HIS A 115 PHE 0.017 0.002 PHE c 399 TYR 0.019 0.002 TYR B 241 ARG 0.007 0.000 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 33) link_NAG-ASN : angle 3.78992 ( 99) link_ALPHA1-6 : bond 0.00748 ( 5) link_ALPHA1-6 : angle 1.88567 ( 15) link_BETA1-4 : bond 0.00607 ( 31) link_BETA1-4 : angle 2.80572 ( 93) link_ALPHA1-2 : bond 0.00286 ( 2) link_ALPHA1-2 : angle 2.25299 ( 6) link_ALPHA1-3 : bond 0.01014 ( 7) link_ALPHA1-3 : angle 2.38028 ( 21) hydrogen bonds : bond 0.04040 ( 447) hydrogen bonds : angle 4.93964 ( 1185) SS BOND : bond 0.00335 ( 23) SS BOND : angle 1.09167 ( 46) covalent geometry : bond 0.00331 (11244) covalent geometry : angle 0.71785 (15226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9243 (tpp) cc_final: 0.7637 (tpp) REVERT: A 194 MET cc_start: 0.9101 (tpp) cc_final: 0.8748 (tpp) REVERT: a 284 MET cc_start: 0.8625 (mtp) cc_final: 0.8057 (mtt) REVERT: a 303 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7804 (tm-30) REVERT: a 311 ASP cc_start: 0.9240 (m-30) cc_final: 0.8884 (t70) REVERT: a 347 ASP cc_start: 0.8325 (p0) cc_final: 0.7639 (p0) REVERT: a 408 ASP cc_start: 0.8350 (m-30) cc_final: 0.8009 (t70) REVERT: B 134 MET cc_start: 0.8578 (tpp) cc_final: 0.7964 (tpp) REVERT: B 192 MET cc_start: 0.8294 (tpt) cc_final: 0.7923 (tpp) REVERT: b 347 ASP cc_start: 0.7896 (p0) cc_final: 0.7599 (p0) REVERT: L 87 PHE cc_start: 0.8123 (m-80) cc_final: 0.7441 (m-10) REVERT: L 89 LEU cc_start: 0.8585 (tp) cc_final: 0.8289 (tp) REVERT: L 97 ASP cc_start: 0.8843 (t0) cc_final: 0.8638 (t0) REVERT: L 98 ASP cc_start: 0.8459 (m-30) cc_final: 0.7997 (m-30) REVERT: L 106 GLN cc_start: 0.7755 (pp30) cc_final: 0.7282 (pp30) REVERT: C 228 GLU cc_start: 0.8076 (pp20) cc_final: 0.7497 (tp30) REVERT: c 361 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8646 (tt) REVERT: c 370 TRP cc_start: 0.7380 (m-10) cc_final: 0.7147 (m-10) outliers start: 28 outliers final: 15 residues processed: 173 average time/residue: 0.2202 time to fit residues: 55.2677 Evaluate side-chains 162 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 0.0470 chunk 100 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.063580 restraints weight = 36423.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066137 restraints weight = 19674.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.067896 restraints weight = 13399.531| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11345 Z= 0.130 Angle : 0.773 12.704 15506 Z= 0.351 Chirality : 0.046 0.294 1918 Planarity : 0.003 0.045 1803 Dihedral : 9.136 59.704 2929 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.31 % Allowed : 13.07 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.06 (0.24), residues: 1231 helix: 0.90 (0.27), residues: 375 sheet: 0.97 (0.34), residues: 229 loop : -0.85 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 283 HIS 0.013 0.001 HIS A 115 PHE 0.014 0.001 PHE c 399 TYR 0.019 0.001 TYR H 55 ARG 0.005 0.000 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 33) link_NAG-ASN : angle 3.56752 ( 99) link_ALPHA1-6 : bond 0.00764 ( 5) link_ALPHA1-6 : angle 1.82740 ( 15) link_BETA1-4 : bond 0.00567 ( 31) link_BETA1-4 : angle 2.58359 ( 93) link_ALPHA1-2 : bond 0.00283 ( 2) link_ALPHA1-2 : angle 2.16610 ( 6) link_ALPHA1-3 : bond 0.01020 ( 7) link_ALPHA1-3 : angle 2.30982 ( 21) hydrogen bonds : bond 0.03774 ( 447) hydrogen bonds : angle 4.86322 ( 1185) SS BOND : bond 0.00310 ( 23) SS BOND : angle 0.87081 ( 46) covalent geometry : bond 0.00275 (11244) covalent geometry : angle 0.68518 (15226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6722 (mtt) REVERT: a 262 PHE cc_start: 0.6604 (p90) cc_final: 0.6151 (p90) REVERT: a 284 MET cc_start: 0.8650 (mtp) cc_final: 0.8120 (mtt) REVERT: a 303 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7696 (tm-30) REVERT: a 311 ASP cc_start: 0.9221 (m-30) cc_final: 0.8867 (t70) REVERT: a 332 MET cc_start: 0.9024 (tmm) cc_final: 0.8809 (tmm) REVERT: a 347 ASP cc_start: 0.8341 (p0) cc_final: 0.7671 (p0) REVERT: a 408 ASP cc_start: 0.8346 (m-30) cc_final: 0.7960 (t70) REVERT: B 134 MET cc_start: 0.8581 (tpp) cc_final: 0.7718 (tpp) REVERT: B 192 MET cc_start: 0.8294 (tpt) cc_final: 0.7919 (tpp) REVERT: B 219 TYR cc_start: 0.8452 (m-80) cc_final: 0.8172 (m-10) REVERT: b 284 MET cc_start: 0.7677 (mtm) cc_final: 0.7410 (mtm) REVERT: b 312 MET cc_start: 0.8743 (mmm) cc_final: 0.8514 (mmm) REVERT: b 347 ASP cc_start: 0.7978 (p0) cc_final: 0.7603 (p0) REVERT: H 96 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7964 (mmm-85) REVERT: L 42 TYR cc_start: 0.8607 (m-80) cc_final: 0.8309 (m-10) REVERT: L 87 PHE cc_start: 0.7999 (m-80) cc_final: 0.7501 (m-10) REVERT: L 89 LEU cc_start: 0.8628 (tp) cc_final: 0.8301 (tp) REVERT: L 97 ASP cc_start: 0.8771 (t0) cc_final: 0.8456 (t0) REVERT: L 98 ASP cc_start: 0.8439 (m-30) cc_final: 0.8026 (m-30) REVERT: L 106 GLN cc_start: 0.7713 (pp30) cc_final: 0.7243 (pp30) REVERT: C 170 HIS cc_start: 0.6295 (t-90) cc_final: 0.6012 (t-170) REVERT: C 228 GLU cc_start: 0.7968 (pp20) cc_final: 0.7638 (tp30) REVERT: c 361 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8678 (tt) REVERT: c 370 TRP cc_start: 0.7325 (m-10) cc_final: 0.7031 (m-10) outliers start: 26 outliers final: 16 residues processed: 174 average time/residue: 0.2326 time to fit residues: 58.3566 Evaluate side-chains 163 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058655 restraints weight = 38592.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061073 restraints weight = 21194.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.062717 restraints weight = 14686.076| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11345 Z= 0.267 Angle : 0.884 13.502 15506 Z= 0.404 Chirality : 0.048 0.332 1918 Planarity : 0.004 0.047 1803 Dihedral : 8.757 54.703 2929 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.49 % Allowed : 13.87 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.10 (0.23), residues: 1231 helix: 0.99 (0.28), residues: 372 sheet: 0.90 (0.35), residues: 221 loop : -1.08 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 52 HIS 0.012 0.002 HIS A 115 PHE 0.017 0.002 PHE L 87 TYR 0.023 0.002 TYR L 107 ARG 0.004 0.001 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 33) link_NAG-ASN : angle 3.86771 ( 99) link_ALPHA1-6 : bond 0.00690 ( 5) link_ALPHA1-6 : angle 1.96408 ( 15) link_BETA1-4 : bond 0.00524 ( 31) link_BETA1-4 : angle 2.67753 ( 93) link_ALPHA1-2 : bond 0.00386 ( 2) link_ALPHA1-2 : angle 2.36747 ( 6) link_ALPHA1-3 : bond 0.00954 ( 7) link_ALPHA1-3 : angle 2.37295 ( 21) hydrogen bonds : bond 0.04383 ( 447) hydrogen bonds : angle 4.92144 ( 1185) SS BOND : bond 0.00419 ( 23) SS BOND : angle 1.28255 ( 46) covalent geometry : bond 0.00609 (11244) covalent geometry : angle 0.79778 (15226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7496 (mtp) cc_final: 0.7141 (mtt) REVERT: A 134 MET cc_start: 0.9284 (tpp) cc_final: 0.7475 (tpp) REVERT: A 162 ILE cc_start: 0.9510 (mt) cc_final: 0.9304 (mm) REVERT: A 192 MET cc_start: 0.9026 (tpp) cc_final: 0.8805 (tpp) REVERT: a 284 MET cc_start: 0.8657 (mtp) cc_final: 0.8043 (mtt) REVERT: a 303 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7643 (tm-30) REVERT: a 311 ASP cc_start: 0.9306 (m-30) cc_final: 0.9062 (t70) REVERT: a 332 MET cc_start: 0.9114 (tmm) cc_final: 0.8625 (tmm) REVERT: a 347 ASP cc_start: 0.8510 (p0) cc_final: 0.8118 (p0) REVERT: a 348 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8365 (mm110) REVERT: a 408 ASP cc_start: 0.8435 (m-30) cc_final: 0.8058 (t70) REVERT: B 134 MET cc_start: 0.8638 (tpp) cc_final: 0.7533 (tpp) REVERT: B 192 MET cc_start: 0.8444 (tpt) cc_final: 0.8020 (tpp) REVERT: b 311 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8550 (t0) REVERT: b 347 ASP cc_start: 0.7979 (p0) cc_final: 0.7715 (p0) REVERT: L 87 PHE cc_start: 0.8090 (m-80) cc_final: 0.7741 (m-10) REVERT: L 89 LEU cc_start: 0.8616 (tp) cc_final: 0.8309 (tp) REVERT: L 97 ASP cc_start: 0.8865 (t0) cc_final: 0.8578 (t0) REVERT: L 98 ASP cc_start: 0.8459 (m-30) cc_final: 0.8108 (m-30) REVERT: L 106 GLN cc_start: 0.8287 (pp30) cc_final: 0.7914 (pp30) REVERT: C 80 MET cc_start: 0.8428 (mpp) cc_final: 0.8206 (mpp) REVERT: C 228 GLU cc_start: 0.8035 (pp20) cc_final: 0.7709 (tp30) REVERT: c 284 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8353 (ptp) REVERT: c 370 TRP cc_start: 0.7700 (m-10) cc_final: 0.7319 (m-10) outliers start: 28 outliers final: 19 residues processed: 163 average time/residue: 0.2296 time to fit residues: 54.2690 Evaluate side-chains 156 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 13 optimal weight: 0.1980 chunk 84 optimal weight: 0.0030 chunk 95 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.060570 restraints weight = 37959.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.063074 restraints weight = 20638.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064785 restraints weight = 14175.929| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11345 Z= 0.150 Angle : 0.773 12.941 15506 Z= 0.354 Chirality : 0.045 0.290 1918 Planarity : 0.003 0.047 1803 Dihedral : 8.120 55.749 2929 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.22 % Allowed : 14.76 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.03 (0.24), residues: 1231 helix: 1.06 (0.27), residues: 373 sheet: 0.97 (0.35), residues: 219 loop : -0.97 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 210 HIS 0.013 0.001 HIS A 115 PHE 0.013 0.002 PHE c 262 TYR 0.023 0.001 TYR B 219 ARG 0.004 0.000 ARG b 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 33) link_NAG-ASN : angle 3.53019 ( 99) link_ALPHA1-6 : bond 0.00742 ( 5) link_ALPHA1-6 : angle 1.89934 ( 15) link_BETA1-4 : bond 0.00548 ( 31) link_BETA1-4 : angle 2.35948 ( 93) link_ALPHA1-2 : bond 0.00131 ( 2) link_ALPHA1-2 : angle 2.10504 ( 6) link_ALPHA1-3 : bond 0.01027 ( 7) link_ALPHA1-3 : angle 2.13224 ( 21) hydrogen bonds : bond 0.03762 ( 447) hydrogen bonds : angle 4.77884 ( 1185) SS BOND : bond 0.00307 ( 23) SS BOND : angle 0.87112 ( 46) covalent geometry : bond 0.00335 (11244) covalent geometry : angle 0.69235 (15226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9307 (tpp) cc_final: 0.7440 (tpp) REVERT: A 192 MET cc_start: 0.9029 (tpp) cc_final: 0.8828 (tpp) REVERT: A 230 HIS cc_start: 0.7628 (m-70) cc_final: 0.7365 (m170) REVERT: a 284 MET cc_start: 0.8676 (mtp) cc_final: 0.8148 (mtt) REVERT: a 303 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7658 (tm-30) REVERT: a 311 ASP cc_start: 0.9235 (m-30) cc_final: 0.9024 (t0) REVERT: a 332 MET cc_start: 0.9129 (tmm) cc_final: 0.8640 (tmm) REVERT: a 347 ASP cc_start: 0.8531 (p0) cc_final: 0.8138 (p0) REVERT: a 348 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8381 (mm110) REVERT: a 408 ASP cc_start: 0.8377 (m-30) cc_final: 0.8010 (t70) REVERT: B 134 MET cc_start: 0.8600 (tpp) cc_final: 0.7457 (tpp) REVERT: B 192 MET cc_start: 0.8354 (tpt) cc_final: 0.7921 (tpp) REVERT: b 311 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8480 (t0) REVERT: b 347 ASP cc_start: 0.8060 (p0) cc_final: 0.7653 (p0) REVERT: L 87 PHE cc_start: 0.8105 (m-80) cc_final: 0.7772 (m-10) REVERT: L 89 LEU cc_start: 0.8588 (tp) cc_final: 0.8265 (tp) REVERT: L 97 ASP cc_start: 0.8779 (t0) cc_final: 0.8473 (t0) REVERT: L 98 ASP cc_start: 0.8320 (m-30) cc_final: 0.8003 (m-30) REVERT: L 106 GLN cc_start: 0.8078 (pp30) cc_final: 0.7681 (pp30) REVERT: C 228 GLU cc_start: 0.7909 (pp20) cc_final: 0.7699 (tp30) REVERT: c 284 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8376 (mtm) REVERT: c 370 TRP cc_start: 0.7559 (m-10) cc_final: 0.7234 (m-10) outliers start: 25 outliers final: 15 residues processed: 167 average time/residue: 0.2213 time to fit residues: 53.2944 Evaluate side-chains 155 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 313 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 51 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 0.0980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.074884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059845 restraints weight = 37765.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.062323 restraints weight = 20584.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.064011 restraints weight = 14147.830| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11345 Z= 0.169 Angle : 0.785 12.918 15506 Z= 0.360 Chirality : 0.046 0.305 1918 Planarity : 0.004 0.048 1803 Dihedral : 7.820 53.666 2929 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.78 % Allowed : 15.82 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.03 (0.24), residues: 1231 helix: 1.08 (0.28), residues: 372 sheet: 0.94 (0.35), residues: 219 loop : -1.06 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 227 HIS 0.014 0.001 HIS A 115 PHE 0.014 0.002 PHE c 262 TYR 0.019 0.002 TYR B 219 ARG 0.003 0.000 ARG a 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 33) link_NAG-ASN : angle 3.47733 ( 99) link_ALPHA1-6 : bond 0.00745 ( 5) link_ALPHA1-6 : angle 1.90680 ( 15) link_BETA1-4 : bond 0.00494 ( 31) link_BETA1-4 : angle 2.36218 ( 93) link_ALPHA1-2 : bond 0.00163 ( 2) link_ALPHA1-2 : angle 2.19027 ( 6) link_ALPHA1-3 : bond 0.00925 ( 7) link_ALPHA1-3 : angle 2.06997 ( 21) hydrogen bonds : bond 0.03810 ( 447) hydrogen bonds : angle 4.78881 ( 1185) SS BOND : bond 0.00330 ( 23) SS BOND : angle 0.89412 ( 46) covalent geometry : bond 0.00382 (11244) covalent geometry : angle 0.70777 (15226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9246 (tpp) cc_final: 0.7253 (tpp) REVERT: A 230 HIS cc_start: 0.7585 (m-70) cc_final: 0.7354 (m170) REVERT: a 284 MET cc_start: 0.8622 (mtp) cc_final: 0.8127 (mtt) REVERT: a 303 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7434 (tm-30) REVERT: a 307 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7792 (mt-10) REVERT: a 311 ASP cc_start: 0.9270 (m-30) cc_final: 0.9065 (t0) REVERT: a 347 ASP cc_start: 0.8488 (p0) cc_final: 0.8157 (p0) REVERT: a 408 ASP cc_start: 0.8411 (m-30) cc_final: 0.8045 (t70) REVERT: B 134 MET cc_start: 0.8596 (tpp) cc_final: 0.7443 (tpp) REVERT: B 192 MET cc_start: 0.8450 (tpt) cc_final: 0.8029 (tpp) REVERT: b 311 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8473 (t0) REVERT: b 312 MET cc_start: 0.8666 (mmm) cc_final: 0.8370 (mmp) REVERT: b 347 ASP cc_start: 0.8033 (p0) cc_final: 0.7798 (p0) REVERT: H 96 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.8071 (mmm-85) REVERT: L 87 PHE cc_start: 0.8040 (m-80) cc_final: 0.7576 (m-10) REVERT: L 89 LEU cc_start: 0.8603 (tp) cc_final: 0.8292 (tp) REVERT: L 97 ASP cc_start: 0.8790 (t0) cc_final: 0.8503 (t0) REVERT: L 98 ASP cc_start: 0.8338 (m-30) cc_final: 0.8040 (m-30) REVERT: L 106 GLN cc_start: 0.8143 (pp30) cc_final: 0.7747 (pp30) REVERT: C 80 MET cc_start: 0.8517 (mpp) cc_final: 0.8313 (mpp) REVERT: C 228 GLU cc_start: 0.7917 (pp20) cc_final: 0.7632 (tp30) REVERT: c 282 ARG cc_start: 0.8059 (tpt90) cc_final: 0.7609 (tpt90) REVERT: c 284 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8348 (mtm) REVERT: c 370 TRP cc_start: 0.7691 (m-10) cc_final: 0.7324 (m-10) outliers start: 20 outliers final: 13 residues processed: 153 average time/residue: 0.2145 time to fit residues: 48.0917 Evaluate side-chains 149 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 354 HIS ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.075432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060209 restraints weight = 38260.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.062692 restraints weight = 21134.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.064373 restraints weight = 14585.174| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11345 Z= 0.151 Angle : 0.762 12.800 15506 Z= 0.351 Chirality : 0.045 0.293 1918 Planarity : 0.003 0.047 1803 Dihedral : 7.628 59.461 2929 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 1.87 % Allowed : 16.36 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.07 (0.24), residues: 1231 helix: 1.15 (0.28), residues: 368 sheet: 0.97 (0.36), residues: 219 loop : -0.96 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 370 HIS 0.015 0.001 HIS A 115 PHE 0.009 0.002 PHE b 318 TYR 0.020 0.001 TYR B 219 ARG 0.002 0.000 ARG a 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 33) link_NAG-ASN : angle 3.38463 ( 99) link_ALPHA1-6 : bond 0.00769 ( 5) link_ALPHA1-6 : angle 1.89241 ( 15) link_BETA1-4 : bond 0.00512 ( 31) link_BETA1-4 : angle 2.28900 ( 93) link_ALPHA1-2 : bond 0.00135 ( 2) link_ALPHA1-2 : angle 2.11931 ( 6) link_ALPHA1-3 : bond 0.00945 ( 7) link_ALPHA1-3 : angle 2.06038 ( 21) hydrogen bonds : bond 0.03601 ( 447) hydrogen bonds : angle 4.77690 ( 1185) SS BOND : bond 0.00294 ( 23) SS BOND : angle 0.80769 ( 46) covalent geometry : bond 0.00341 (11244) covalent geometry : angle 0.68702 (15226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9249 (tpp) cc_final: 0.7274 (tpp) REVERT: a 284 MET cc_start: 0.8652 (mtp) cc_final: 0.8037 (mtp) REVERT: a 347 ASP cc_start: 0.8535 (p0) cc_final: 0.8009 (p0) REVERT: a 408 ASP cc_start: 0.8403 (m-30) cc_final: 0.8041 (t70) REVERT: B 134 MET cc_start: 0.8591 (tpp) cc_final: 0.7442 (tpp) REVERT: B 192 MET cc_start: 0.8450 (tpt) cc_final: 0.8000 (tpp) REVERT: b 311 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8524 (t0) REVERT: b 312 MET cc_start: 0.8637 (mmm) cc_final: 0.8386 (mmp) REVERT: b 347 ASP cc_start: 0.8090 (p0) cc_final: 0.7759 (p0) REVERT: L 89 LEU cc_start: 0.8602 (tp) cc_final: 0.8288 (tp) REVERT: L 97 ASP cc_start: 0.8771 (t0) cc_final: 0.8478 (t0) REVERT: L 98 ASP cc_start: 0.8317 (m-30) cc_final: 0.8040 (m-30) REVERT: L 106 GLN cc_start: 0.8108 (pp30) cc_final: 0.7713 (pp30) REVERT: C 80 MET cc_start: 0.8369 (mpp) cc_final: 0.8164 (mpp) REVERT: C 170 HIS cc_start: 0.6766 (t-90) cc_final: 0.6479 (t-170) REVERT: c 317 ASP cc_start: 0.8774 (t0) cc_final: 0.8554 (t0) REVERT: c 370 TRP cc_start: 0.7672 (m-10) cc_final: 0.7206 (m-90) outliers start: 21 outliers final: 15 residues processed: 150 average time/residue: 0.2264 time to fit residues: 49.5756 Evaluate side-chains 146 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 319 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 335 GLN C 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.072236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.057281 restraints weight = 38258.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.059633 restraints weight = 21097.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061209 restraints weight = 14632.254| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11345 Z= 0.289 Angle : 0.917 13.106 15506 Z= 0.423 Chirality : 0.049 0.336 1918 Planarity : 0.004 0.048 1803 Dihedral : 8.173 59.988 2929 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 1.69 % Allowed : 16.53 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1231 helix: 0.99 (0.28), residues: 372 sheet: 0.59 (0.35), residues: 221 loop : -1.21 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP b 370 HIS 0.013 0.002 HIS A 115 PHE 0.018 0.003 PHE C 147 TYR 0.021 0.002 TYR B 219 ARG 0.005 0.001 ARG c 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 33) link_NAG-ASN : angle 3.63286 ( 99) link_ALPHA1-6 : bond 0.00699 ( 5) link_ALPHA1-6 : angle 2.06835 ( 15) link_BETA1-4 : bond 0.00512 ( 31) link_BETA1-4 : angle 2.47595 ( 93) link_ALPHA1-2 : bond 0.00358 ( 2) link_ALPHA1-2 : angle 2.41936 ( 6) link_ALPHA1-3 : bond 0.00828 ( 7) link_ALPHA1-3 : angle 2.09072 ( 21) hydrogen bonds : bond 0.04528 ( 447) hydrogen bonds : angle 5.03375 ( 1185) SS BOND : bond 0.00484 ( 23) SS BOND : angle 1.14111 ( 46) covalent geometry : bond 0.00659 (11244) covalent geometry : angle 0.84645 (15226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9316 (tpp) cc_final: 0.7378 (tpp) REVERT: a 262 PHE cc_start: 0.7547 (p90) cc_final: 0.6962 (p90) REVERT: a 284 MET cc_start: 0.8599 (mtp) cc_final: 0.8057 (mtt) REVERT: a 303 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7517 (tm-30) REVERT: a 347 ASP cc_start: 0.8570 (p0) cc_final: 0.8247 (p0) REVERT: a 408 ASP cc_start: 0.8398 (m-30) cc_final: 0.8028 (t70) REVERT: B 134 MET cc_start: 0.8627 (tpp) cc_final: 0.7404 (tpp) REVERT: B 192 MET cc_start: 0.8602 (tpt) cc_final: 0.8227 (tpp) REVERT: b 347 ASP cc_start: 0.8121 (p0) cc_final: 0.7921 (p0) REVERT: H 96 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8180 (mmm-85) REVERT: L 89 LEU cc_start: 0.8552 (tp) cc_final: 0.8242 (tp) REVERT: L 97 ASP cc_start: 0.8857 (t0) cc_final: 0.8623 (t0) REVERT: L 98 ASP cc_start: 0.8300 (m-30) cc_final: 0.8053 (m-30) REVERT: L 106 GLN cc_start: 0.8441 (pp30) cc_final: 0.8099 (pp30) REVERT: C 80 MET cc_start: 0.8554 (mpp) cc_final: 0.8326 (mpp) REVERT: c 282 ARG cc_start: 0.8036 (tpt90) cc_final: 0.7584 (tpt90) REVERT: c 284 MET cc_start: 0.8450 (mtm) cc_final: 0.8161 (pmm) REVERT: c 317 ASP cc_start: 0.8784 (t0) cc_final: 0.8557 (t0) REVERT: c 370 TRP cc_start: 0.7957 (m-10) cc_final: 0.7720 (m-10) outliers start: 19 outliers final: 16 residues processed: 142 average time/residue: 0.2259 time to fit residues: 46.8982 Evaluate side-chains 144 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.075606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060861 restraints weight = 37182.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.063361 restraints weight = 19989.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.065048 restraints weight = 13633.246| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11345 Z= 0.135 Angle : 0.775 12.834 15506 Z= 0.358 Chirality : 0.045 0.307 1918 Planarity : 0.003 0.047 1803 Dihedral : 7.448 59.146 2929 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 1.69 % Allowed : 16.62 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.05 (0.24), residues: 1231 helix: 1.05 (0.28), residues: 375 sheet: 0.75 (0.36), residues: 221 loop : -1.00 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP b 370 HIS 0.016 0.001 HIS A 115 PHE 0.017 0.001 PHE c 309 TYR 0.020 0.001 TYR B 219 ARG 0.003 0.000 ARG c 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 33) link_NAG-ASN : angle 3.29491 ( 99) link_ALPHA1-6 : bond 0.00791 ( 5) link_ALPHA1-6 : angle 1.85087 ( 15) link_BETA1-4 : bond 0.00556 ( 31) link_BETA1-4 : angle 2.16191 ( 93) link_ALPHA1-2 : bond 0.00121 ( 2) link_ALPHA1-2 : angle 2.01560 ( 6) link_ALPHA1-3 : bond 0.00926 ( 7) link_ALPHA1-3 : angle 1.95265 ( 21) hydrogen bonds : bond 0.03571 ( 447) hydrogen bonds : angle 4.78737 ( 1185) SS BOND : bond 0.00248 ( 23) SS BOND : angle 0.74076 ( 46) covalent geometry : bond 0.00304 (11244) covalent geometry : angle 0.70805 (15226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4351.87 seconds wall clock time: 79 minutes 45.10 seconds (4785.10 seconds total)