Starting phenix.real_space_refine on Sun Dec 29 19:01:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eji_28183/12_2024/8eji_28183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eji_28183/12_2024/8eji_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_28183/12_2024/8eji_28183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eji_28183/12_2024/8eji_28183.map" model { file = "/net/cci-nas-00/data/ceres_data/8eji_28183/12_2024/8eji_28183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eji_28183/12_2024/8eji_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-5532/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: 5.67, per 1000 atoms: 0.51 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: 4.19 Conformation dependent library (CDL) restraints added in 2.1 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: 1.28 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: 3.49 Time building geometry restraints manager: 4.64 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: 0.000 Normalize map: mean=0, sd=1: 9.070 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 30.070 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.600 ------------------------------------------------------------------------------- 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 : 0.022 0.134 11244 Z= 1.378 Angle : 1.848 13.663 15226 Z= 1.168 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 *********************** 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 : 1.262 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: 0.2816 time to fit residues: 126.4154 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 : 1.332 ------------------------------------------------------------------------------- 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: 8.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 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 ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11244 Z= 0.259 Angle : 0.888 16.068 15226 Z= 0.437 Chirality : 0.053 0.331 1918 Planarity : 0.004 0.032 1803 Dihedral : 14.408 89.448 2929 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.26 % Rotamer: Outliers : 2.40 % Allowed : 9.87 % Favored : 87.73 % 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: 0.57 (0.26), residues: 370 sheet: 1.05 (0.36), residues: 198 loop : -0.47 (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 *********************** 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 221 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9075 (tpp) cc_final: 0.7787 (tpp) REVERT: A 150 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: A 210 TRP cc_start: 0.7513 (t60) cc_final: 0.7288 (t60) REVERT: a 284 MET cc_start: 0.8879 (mtp) cc_final: 0.8508 (mtt) REVERT: a 311 ASP cc_start: 0.9054 (m-30) cc_final: 0.8750 (t70) REVERT: a 332 MET cc_start: 0.8903 (tmm) cc_final: 0.8116 (tmm) REVERT: a 347 ASP cc_start: 0.8146 (p0) cc_final: 0.7461 (p0) REVERT: a 405 GLN cc_start: 0.8910 (tp40) cc_final: 0.8660 (tp40) REVERT: a 408 ASP cc_start: 0.8435 (m-30) cc_final: 0.8046 (t70) REVERT: B 140 PHE cc_start: 0.8832 (t80) cc_final: 0.8490 (t80) REVERT: B 189 GLN cc_start: 0.8964 (mt0) cc_final: 0.8630 (tt0) REVERT: B 192 MET cc_start: 0.8823 (tpt) cc_final: 0.8613 (tpp) REVERT: B 214 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7111 (pmm) REVERT: b 312 MET cc_start: 0.9011 (mmm) cc_final: 0.8811 (mmm) REVERT: b 347 ASP cc_start: 0.7560 (p0) cc_final: 0.7183 (p0) REVERT: L 106 GLN cc_start: 0.7952 (pp30) cc_final: 0.7670 (pp30) REVERT: c 312 MET cc_start: 0.8993 (mmm) cc_final: 0.8235 (mmm) REVERT: c 370 TRP cc_start: 0.7802 (m-10) cc_final: 0.7299 (m-10) outliers start: 27 outliers final: 10 residues processed: 209 average time/residue: 0.2344 time to fit residues: 69.9320 Evaluate side-chains 158 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 C residue 245 LEU 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 62 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 179 HIS ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 185 ASN b 348 GLN L 43 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11244 Z= 0.277 Angle : 0.799 10.992 15226 Z= 0.389 Chirality : 0.049 0.323 1918 Planarity : 0.004 0.043 1803 Dihedral : 11.499 79.254 2929 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.67 % Allowed : 12.44 % Favored : 84.89 % 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: -0.02 (0.23), residues: 1231 helix: 0.75 (0.27), residues: 375 sheet: 0.91 (0.34), residues: 223 loop : -0.82 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 283 HIS 0.011 0.001 HIS A 179 PHE 0.021 0.002 PHE c 399 TYR 0.021 0.002 TYR A 62 ARG 0.008 0.001 ARG b 314 *********************** 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 188 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.258 Fit side-chains 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: 0.7897 (tpp) REVERT: a 284 MET cc_start: 0.8953 (mtp) cc_final: 0.8602 (mtt) REVERT: a 311 ASP cc_start: 0.9123 (m-30) cc_final: 0.8870 (t70) REVERT: a 332 MET cc_start: 0.9139 (tmm) cc_final: 0.7896 (tmm) REVERT: a 347 ASP cc_start: 0.8198 (p0) cc_final: 0.7777 (p0) REVERT: a 382 LEU cc_start: 0.9316 (tt) cc_final: 0.9095 (tt) REVERT: a 408 ASP cc_start: 0.8363 (m-30) cc_final: 0.8004 (t70) REVERT: B 192 MET cc_start: 0.8789 (tpt) cc_final: 0.8491 (tpp) REVERT: L 87 PHE cc_start: 0.8237 (m-80) cc_final: 0.7884 (m-10) REVERT: L 97 ASP cc_start: 0.8753 (t0) cc_final: 0.8447 (t0) REVERT: C 251 ASP cc_start: 0.7923 (m-30) cc_final: 0.7722 (m-30) REVERT: c 361 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8538 (tp) REVERT: c 370 TRP cc_start: 0.7861 (m-10) cc_final: 0.7641 (m-10) outliers start: 30 outliers final: 21 residues processed: 174 average time/residue: 0.2429 time to fit residues: 60.0012 Evaluate side-chains 159 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS 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 70 THR 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 81 ARG 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 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 411 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 110 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** C 93 HIS ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11244 Z= 0.222 Angle : 0.736 9.678 15226 Z= 0.358 Chirality : 0.047 0.308 1918 Planarity : 0.004 0.042 1803 Dihedral : 10.088 71.121 2929 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.76 % Allowed : 13.07 % Favored : 84.18 % 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: -0.01 (0.23), residues: 1231 helix: 0.90 (0.27), residues: 375 sheet: 0.89 (0.34), residues: 226 loop : -0.91 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 210 HIS 0.011 0.001 HIS A 115 PHE 0.014 0.002 PHE c 399 TYR 0.019 0.002 TYR B 241 ARG 0.003 0.000 ARG b 314 *********************** 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 188 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 284 MET cc_start: 0.8930 (mtp) cc_final: 0.8582 (mtt) REVERT: a 303 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7931 (tm-30) REVERT: a 311 ASP cc_start: 0.9107 (m-30) cc_final: 0.8849 (t70) REVERT: a 347 ASP cc_start: 0.8210 (p0) cc_final: 0.7652 (p0) REVERT: a 408 ASP cc_start: 0.8321 (m-30) cc_final: 0.8017 (t70) REVERT: B 134 MET cc_start: 0.8373 (tpp) cc_final: 0.8042 (ttm) REVERT: B 192 MET cc_start: 0.8806 (tpt) cc_final: 0.8449 (tpp) REVERT: b 284 MET cc_start: 0.8055 (mtp) cc_final: 0.7797 (mtm) REVERT: b 347 ASP cc_start: 0.7761 (p0) cc_final: 0.7474 (p0) REVERT: L 87 PHE cc_start: 0.8227 (m-80) cc_final: 0.7750 (m-10) REVERT: L 97 ASP cc_start: 0.8777 (t0) cc_final: 0.8419 (t0) REVERT: L 106 GLN cc_start: 0.7910 (pp30) cc_final: 0.7660 (pp30) REVERT: C 228 GLU cc_start: 0.7987 (pp20) cc_final: 0.7473 (tp30) REVERT: c 361 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8617 (tt) REVERT: c 370 TRP cc_start: 0.7677 (m-10) cc_final: 0.7423 (m-10) outliers start: 31 outliers final: 15 residues processed: 175 average time/residue: 0.2373 time to fit residues: 59.8580 Evaluate side-chains 156 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 270 GLU 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 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 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 67 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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** a 354 HIS C 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11244 Z= 0.204 Angle : 0.702 8.485 15226 Z= 0.340 Chirality : 0.047 0.298 1918 Planarity : 0.004 0.044 1803 Dihedral : 9.046 59.741 2929 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.93 % Allowed : 13.42 % 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: 0.05 (0.24), residues: 1231 helix: 0.97 (0.27), residues: 375 sheet: 0.87 (0.34), residues: 229 loop : -0.86 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 210 HIS 0.012 0.001 HIS A 115 PHE 0.015 0.002 PHE L 87 TYR 0.019 0.002 TYR B 219 ARG 0.007 0.000 ARG H 81 *********************** 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: 33 poor density : 154 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7741 (mtt) cc_final: 0.7465 (mtt) REVERT: A 134 MET cc_start: 0.9189 (tpp) cc_final: 0.7646 (tpp) REVERT: A 203 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8421 (tp) REVERT: a 262 PHE cc_start: 0.7118 (p90) cc_final: 0.6644 (p90) REVERT: a 284 MET cc_start: 0.8879 (mtp) cc_final: 0.8502 (mtp) REVERT: a 303 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7815 (tm-30) REVERT: a 311 ASP cc_start: 0.9106 (m-30) cc_final: 0.8866 (t0) REVERT: a 332 MET cc_start: 0.9163 (tmm) cc_final: 0.8654 (tmm) REVERT: a 347 ASP cc_start: 0.8319 (p0) cc_final: 0.7731 (p0) REVERT: a 408 ASP cc_start: 0.8301 (m-30) cc_final: 0.7982 (t70) REVERT: B 94 TYR cc_start: 0.8474 (m-80) cc_final: 0.8268 (m-80) REVERT: B 192 MET cc_start: 0.8814 (tpt) cc_final: 0.8352 (tpp) REVERT: L 87 PHE cc_start: 0.8159 (m-80) cc_final: 0.7835 (m-10) REVERT: L 97 ASP cc_start: 0.8815 (t0) cc_final: 0.8413 (t0) REVERT: C 228 GLU cc_start: 0.7886 (pp20) cc_final: 0.7593 (tp30) REVERT: c 284 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8414 (ptp) REVERT: c 300 LYS cc_start: 0.9220 (mmtp) cc_final: 0.9009 (mtmt) REVERT: c 370 TRP cc_start: 0.7639 (m-10) cc_final: 0.7338 (m-10) outliers start: 33 outliers final: 19 residues processed: 174 average time/residue: 0.2232 time to fit residues: 56.6269 Evaluate side-chains 160 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 270 GLU Chi-restraints excluded: chain B residue 65 VAL 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 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 114 ASN Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 286 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 107 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11244 Z= 0.218 Angle : 0.695 8.095 15226 Z= 0.337 Chirality : 0.046 0.299 1918 Planarity : 0.003 0.046 1803 Dihedral : 8.320 52.571 2929 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.67 % Allowed : 13.69 % 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: 0.09 (0.24), residues: 1231 helix: 1.03 (0.27), residues: 375 sheet: 0.77 (0.34), residues: 237 loop : -0.83 (0.24), residues: 619 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 0.012 0.001 PHE L 87 TYR 0.016 0.001 TYR B 219 ARG 0.005 0.000 ARG H 81 *********************** 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 176 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7494 (mtt) REVERT: A 134 MET cc_start: 0.9286 (tpp) cc_final: 0.7636 (tpp) REVERT: a 284 MET cc_start: 0.8841 (mtp) cc_final: 0.8477 (mtp) REVERT: a 303 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7794 (tm-30) REVERT: a 332 MET cc_start: 0.9220 (tmm) cc_final: 0.8680 (tmm) REVERT: a 347 ASP cc_start: 0.8385 (p0) cc_final: 0.7836 (p0) REVERT: a 408 ASP cc_start: 0.8318 (m-30) cc_final: 0.7978 (t70) REVERT: B 192 MET cc_start: 0.8854 (tpt) cc_final: 0.8449 (tpp) REVERT: L 87 PHE cc_start: 0.8236 (m-80) cc_final: 0.7832 (m-10) REVERT: L 97 ASP cc_start: 0.8773 (t0) cc_final: 0.8361 (t0) REVERT: C 228 GLU cc_start: 0.7839 (pp20) cc_final: 0.7623 (tp30) REVERT: c 370 TRP cc_start: 0.7726 (m-10) cc_final: 0.7415 (m-10) outliers start: 30 outliers final: 18 residues processed: 167 average time/residue: 0.2372 time to fit residues: 56.6611 Evaluate side-chains 153 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 270 GLU Chi-restraints excluded: chain B residue 65 VAL 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 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 155 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 361 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS b 335 GLN ** c 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11244 Z= 0.223 Angle : 0.701 7.314 15226 Z= 0.340 Chirality : 0.046 0.294 1918 Planarity : 0.003 0.042 1803 Dihedral : 7.932 53.736 2929 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.13 % Allowed : 14.76 % Favored : 83.11 % 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: 0.12 (0.24), residues: 1231 helix: 1.11 (0.27), residues: 375 sheet: 0.76 (0.34), residues: 235 loop : -0.83 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 283 HIS 0.012 0.001 HIS A 115 PHE 0.017 0.002 PHE c 262 TYR 0.015 0.001 TYR B 219 ARG 0.004 0.000 ARG H 81 *********************** 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 173 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9262 (tpp) cc_final: 0.7688 (tpp) REVERT: a 284 MET cc_start: 0.8832 (mtp) cc_final: 0.8492 (mtp) REVERT: a 303 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7720 (tm-30) REVERT: a 332 MET cc_start: 0.9212 (tmm) cc_final: 0.8685 (tmm) REVERT: a 347 ASP cc_start: 0.8330 (p0) cc_final: 0.8007 (p0) REVERT: a 408 ASP cc_start: 0.8330 (m-30) cc_final: 0.7972 (t70) REVERT: B 192 MET cc_start: 0.8867 (tpt) cc_final: 0.8455 (tpp) REVERT: L 87 PHE cc_start: 0.8292 (m-80) cc_final: 0.8062 (m-10) REVERT: L 97 ASP cc_start: 0.8722 (t0) cc_final: 0.8295 (t0) REVERT: C 153 MET cc_start: 0.8859 (tmm) cc_final: 0.8429 (tmm) REVERT: C 228 GLU cc_start: 0.7810 (pp20) cc_final: 0.7606 (tp30) REVERT: c 348 GLN cc_start: 0.8640 (mm110) cc_final: 0.7802 (mm110) REVERT: c 370 TRP cc_start: 0.7807 (m-10) cc_final: 0.7474 (m-10) outliers start: 24 outliers final: 18 residues processed: 165 average time/residue: 0.2302 time to fit residues: 55.2147 Evaluate side-chains 149 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 270 GLU Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL 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 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 187 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS ** L 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11244 Z= 0.202 Angle : 0.688 7.479 15226 Z= 0.336 Chirality : 0.046 0.284 1918 Planarity : 0.003 0.039 1803 Dihedral : 7.713 59.598 2929 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.04 % Allowed : 15.20 % Favored : 82.76 % 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: 0.17 (0.24), residues: 1231 helix: 1.16 (0.28), residues: 375 sheet: 0.81 (0.35), residues: 235 loop : -0.83 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 227 HIS 0.014 0.001 HIS A 115 PHE 0.024 0.002 PHE c 262 TYR 0.015 0.001 TYR B 219 ARG 0.012 0.000 ARG c 314 *********************** 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 171 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 284 MET cc_start: 0.8803 (mtp) cc_final: 0.8505 (mtp) REVERT: a 303 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7678 (tm-30) REVERT: a 408 ASP cc_start: 0.8300 (m-30) cc_final: 0.8002 (t70) REVERT: B 192 MET cc_start: 0.8856 (tpt) cc_final: 0.8467 (tpp) REVERT: B 219 TYR cc_start: 0.8772 (m-80) cc_final: 0.8489 (m-80) REVERT: L 87 PHE cc_start: 0.8259 (m-80) cc_final: 0.7952 (m-10) REVERT: L 89 LEU cc_start: 0.8326 (tp) cc_final: 0.8045 (tp) REVERT: L 97 ASP cc_start: 0.8759 (t0) cc_final: 0.8363 (t0) REVERT: C 228 GLU cc_start: 0.7790 (pp20) cc_final: 0.7544 (tp30) REVERT: c 370 TRP cc_start: 0.7792 (m-10) cc_final: 0.7449 (m-10) outliers start: 23 outliers final: 18 residues processed: 161 average time/residue: 0.2242 time to fit residues: 52.2992 Evaluate side-chains 152 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 270 GLU Chi-restraints excluded: chain a residue 345 ILE 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 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 155 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 263 THR 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 103 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11244 Z= 0.320 Angle : 0.761 10.946 15226 Z= 0.371 Chirality : 0.048 0.313 1918 Planarity : 0.004 0.039 1803 Dihedral : 7.823 57.326 2929 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.96 % Allowed : 15.73 % Favored : 82.31 % 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: 1.10 (0.28), residues: 375 sheet: 0.96 (0.35), residues: 219 loop : -1.00 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 210 HIS 0.013 0.001 HIS A 115 PHE 0.019 0.002 PHE c 262 TYR 0.018 0.002 TYR L 107 ARG 0.006 0.001 ARG c 314 *********************** 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: 22 poor density : 136 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9176 (tpp) cc_final: 0.7715 (tpp) REVERT: a 284 MET cc_start: 0.8844 (mtp) cc_final: 0.8563 (mtt) REVERT: a 303 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7756 (tm-30) REVERT: a 408 ASP cc_start: 0.8311 (m-30) cc_final: 0.7989 (t70) REVERT: B 192 MET cc_start: 0.8952 (tpt) cc_final: 0.8552 (tpp) REVERT: b 347 ASP cc_start: 0.7812 (p0) cc_final: 0.7501 (p0) REVERT: L 87 PHE cc_start: 0.8353 (m-80) cc_final: 0.8147 (m-10) REVERT: L 89 LEU cc_start: 0.8301 (tp) cc_final: 0.7995 (tp) REVERT: L 97 ASP cc_start: 0.8776 (t0) cc_final: 0.8326 (t0) REVERT: c 282 ARG cc_start: 0.8300 (tpt90) cc_final: 0.7921 (tpt90) REVERT: c 370 TRP cc_start: 0.8069 (m-10) cc_final: 0.7631 (m-10) outliers start: 22 outliers final: 18 residues processed: 150 average time/residue: 0.2303 time to fit residues: 50.3754 Evaluate side-chains 147 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 270 GLU Chi-restraints excluded: chain a residue 345 ILE 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 355 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 95 LEU 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 187 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 359 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 71 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 0.0050 chunk 122 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.7154 ------------------------------------------------------------------------------- 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 C 141 HIS C 170 HIS c 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11244 Z= 0.200 Angle : 0.719 11.351 15226 Z= 0.352 Chirality : 0.045 0.280 1918 Planarity : 0.003 0.037 1803 Dihedral : 7.478 58.833 2929 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 1.69 % Allowed : 16.00 % Favored : 82.31 % 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: 0.08 (0.24), residues: 1231 helix: 1.05 (0.27), residues: 375 sheet: 1.00 (0.36), residues: 219 loop : -0.92 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 210 HIS 0.015 0.001 HIS A 115 PHE 0.012 0.001 PHE c 262 TYR 0.021 0.001 TYR B 200 ARG 0.006 0.000 ARG c 314 ********************** 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 160 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9150 (tpp) cc_final: 0.7702 (tpp) REVERT: a 284 MET cc_start: 0.8803 (mtp) cc_final: 0.8488 (mtp) REVERT: a 408 ASP cc_start: 0.8321 (m-30) cc_final: 0.8024 (t70) REVERT: B 192 MET cc_start: 0.8910 (tpt) cc_final: 0.8495 (tpp) REVERT: L 87 PHE cc_start: 0.8306 (m-80) cc_final: 0.8093 (m-10) REVERT: L 89 LEU cc_start: 0.8309 (tp) cc_final: 0.8030 (tp) REVERT: L 97 ASP cc_start: 0.8795 (t0) cc_final: 0.8395 (t0) REVERT: c 348 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8282 (mm110) REVERT: c 370 TRP cc_start: 0.7827 (m-10) cc_final: 0.7429 (m-90) outliers start: 19 outliers final: 17 residues processed: 152 average time/residue: 0.2304 time to fit residues: 50.6839 Evaluate side-chains 150 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain a residue 270 GLU Chi-restraints excluded: chain a residue 345 ILE 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 349 LEU 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 155 CYS Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 359 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 29 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 40 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 85 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.076727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061973 restraints weight = 36730.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.064506 restraints weight = 19624.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.066231 restraints weight = 13313.607| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11244 Z= 0.202 Angle : 0.711 10.574 15226 Z= 0.348 Chirality : 0.045 0.284 1918 Planarity : 0.003 0.037 1803 Dihedral : 7.144 54.156 2929 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 1.69 % Allowed : 16.44 % Favored : 81.87 % 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: 0.15 (0.24), residues: 1231 helix: 1.14 (0.27), residues: 375 sheet: 0.93 (0.36), residues: 227 loop : -0.86 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 370 HIS 0.016 0.001 HIS A 115 PHE 0.013 0.001 PHE b 316 TYR 0.020 0.001 TYR B 200 ARG 0.003 0.000 ARG H 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.36 seconds wall clock time: 42 minutes 40.03 seconds (2560.03 seconds total)