Starting phenix.real_space_refine on Fri Feb 14 09:13:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ck7_45643/02_2025/9ck7_45643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ck7_45643/02_2025/9ck7_45643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ck7_45643/02_2025/9ck7_45643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ck7_45643/02_2025/9ck7_45643.map" model { file = "/net/cci-nas-00/data/ceres_data/9ck7_45643/02_2025/9ck7_45643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ck7_45643/02_2025/9ck7_45643.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 6246 2.51 5 N 1649 2.21 5 O 2041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 595 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'TRANS': 118} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'UNK:plan-1': 119} Unresolved non-hydrogen planarities: 119 Chain: "L" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "a" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1171 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain breaks: 2 Chain: "b" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1173 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain breaks: 2 Chain: "c" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1163 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Chain: "D" 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: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.85, per 1000 atoms: 0.88 Number of scatterers: 10026 At special positions: 0 Unit cell: (123.25, 88.45, 95.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2041 8.00 N 1649 7.00 C 6246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " NAG-ASN " NAG A 301 " - " ASN A 89 " " NAG A 302 " - " ASN A 99 " " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 224 " " NAG C 301 " - " ASN C 99 " " NAG C 302 " - " ASN C 119 " " NAG C 303 " - " ASN C 89 " " NAG D 1 " - " ASN A 109 " " NAG E 1 " - " ASN A 119 " " NAG F 1 " - " ASN A 79 " " NAG G 1 " - " ASN A 167 " " NAG I 1 " - " ASN A 224 " " NAG J 1 " - " ASN B 79 " " NAG K 1 " - " ASN B 99 " " NAG M 1 " - " ASN B 109 " " NAG N 1 " - " ASN B 119 " " NAG O 1 " - " ASN B 167 " " NAG P 1 " - " ASN C 79 " " NAG Q 1 " - " ASN C 109 " " NAG R 1 " - " ASN C 167 " " NAG S 1 " - " ASN C 224 " " NAG T 1 " - " ASN a 365 " " NAG U 1 " - " ASN b 365 " " NAG V 1 " - " ASN b 373 " " NAG W 1 " - " ASN c 365 " " NAG a 701 " - " ASN a 373 " " NAG a 702 " - " ASN a 390 " " NAG a 703 " - " ASN a 395 " " NAG b 701 " - " ASN b 395 " " NAG b 702 " - " ASN b 390 " " NAG c 701 " - " ASN c 373 " " NAG c 702 " - " ASN c 390 " " NAG c 703 " - " ASN c 395 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 900.0 milliseconds 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 15 sheets defined 38.9% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.812A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.985A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 4.503A pdb=" N ILE A 201 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 203 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.712A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.949A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.631A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.973A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.527A pdb=" N LEU C 78 " --> pdb=" O MET C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 144 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 182 through 195 removed outlier: 3.966A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 238 through 246 removed outlier: 4.306A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'a' and resid 281 through 285 removed outlier: 3.658A pdb=" N LEU a 285 " --> pdb=" O ARG a 282 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 304 removed outlier: 3.797A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU a 303 " --> pdb=" O ALA a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 326 removed outlier: 3.874A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 345 removed outlier: 6.097A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 359 Processing helix chain 'a' and resid 399 through 412 removed outlier: 3.507A pdb=" N ILE a 403 " --> pdb=" O PHE a 399 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR a 412 " --> pdb=" O ASP a 408 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 304 Processing helix chain 'b' and resid 307 through 325 removed outlier: 4.144A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.490A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.622A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 412 removed outlier: 3.776A pdb=" N ILE b 403 " --> pdb=" O PHE b 399 " (cutoff:3.500A) Processing helix chain 'c' and resid 281 through 285 removed outlier: 3.605A pdb=" N LEU c 285 " --> pdb=" O ARG c 282 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 304 removed outlier: 3.669A pdb=" N VAL c 298 " --> pdb=" O GLY c 294 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN c 302 " --> pdb=" O VAL c 298 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU c 303 " --> pdb=" O ALA c 299 " (cutoff:3.500A) Processing helix chain 'c' and resid 311 through 325 Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.464A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.696A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 412 removed outlier: 3.586A pdb=" N THR c 412 " --> pdb=" O ASP c 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.764A pdb=" N GLU A 67 " --> pdb=" O ASN a 373 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN a 373 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 69 " --> pdb=" O TYR a 371 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR a 371 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 87 removed outlier: 7.432A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 4 removed outlier: 3.857A pdb=" N UNK H 3 " --> pdb=" O UNK H 25 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N UNK H 76 " --> pdb=" O UNK H 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.805A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N UNK H 49 " --> pdb=" O UNK H 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N UNK H 90 " --> pdb=" O UNK H 105 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N UNK H 105 " --> pdb=" O UNK H 90 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N UNK H 92 " --> pdb=" O UNK H 103 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N UNK H 103 " --> pdb=" O UNK H 92 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N UNK H 94 " --> pdb=" O UNK H 101 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK H 100F" --> pdb=" O UNK H 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.858A pdb=" N UNK L 11 " --> pdb=" O UNK L 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.569A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 279 through 280 Processing sheet with id=AB4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB5, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AB6, first strand: chain 'c' and resid 388 through 389 356 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2571 1.33 - 1.46: 3159 1.46 - 1.59: 4324 1.59 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 10192 Sorted by residual: bond pdb=" N HIS B 230 " pdb=" CA HIS B 230 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.49e+00 bond pdb=" N GLU B 228 " pdb=" CA GLU B 228 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.09e-02 8.42e+03 7.81e+00 bond pdb=" N PHE B 233 " pdb=" CA PHE B 233 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.28e-02 6.10e+03 6.99e+00 bond pdb=" N ASN B 146 " pdb=" CA ASN B 146 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.17e+00 bond pdb=" N GLN B 232 " pdb=" CA GLN B 232 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.04e+00 ... (remaining 10187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 12938 1.79 - 3.58: 714 3.58 - 5.36: 143 5.36 - 7.15: 35 7.15 - 8.94: 5 Bond angle restraints: 13835 Sorted by residual: angle pdb=" CA ASP B 229 " pdb=" C ASP B 229 " pdb=" O ASP B 229 " ideal model delta sigma weight residual 122.64 117.77 4.87 1.25e+00 6.40e-01 1.52e+01 angle pdb=" CB GLN b 405 " pdb=" CG GLN b 405 " pdb=" CD GLN b 405 " ideal model delta sigma weight residual 112.60 118.92 -6.32 1.70e+00 3.46e-01 1.38e+01 angle pdb=" CA GLU B 100 " pdb=" CB GLU B 100 " pdb=" CG GLU B 100 " ideal model delta sigma weight residual 114.10 120.98 -6.88 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C PRO B 145 " pdb=" N ASN B 146 " pdb=" CA ASN B 146 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" CA GLN B 232 " pdb=" C GLN B 232 " pdb=" O GLN B 232 " ideal model delta sigma weight residual 120.55 117.02 3.53 1.06e+00 8.90e-01 1.11e+01 ... (remaining 13830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 6454 21.80 - 43.61: 296 43.61 - 65.41: 56 65.41 - 87.21: 24 87.21 - 109.02: 9 Dihedral angle restraints: 6839 sinusoidal: 3206 harmonic: 3633 Sorted by residual: dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS b 360 " pdb=" CB CYS b 360 " ideal model delta sinusoidal sigma weight residual -86.00 -162.05 76.05 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS A 180 " pdb=" SG CYS A 180 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual 93.00 155.37 -62.37 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS c 360 " pdb=" CB CYS c 360 " ideal model delta sinusoidal sigma weight residual -86.00 -134.05 48.05 1 1.00e+01 1.00e-02 3.18e+01 ... (remaining 6836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1716 0.134 - 0.267: 31 0.267 - 0.400: 4 0.400 - 0.534: 4 0.534 - 0.667: 2 Chirality restraints: 1757 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-02 2.50e+03 6.32e+02 chirality pdb=" C1 MAN J 4 " pdb=" O6 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 5.01e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.41e+02 ... (remaining 1754 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 701 " 0.359 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG b 701 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG b 701 " 0.086 2.00e-02 2.50e+03 pdb=" N2 NAG b 701 " -0.546 2.00e-02 2.50e+03 pdb=" O7 NAG b 701 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.351 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG F 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.147 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG J 2 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.069 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.519 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.187 2.00e-02 2.50e+03 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 200 2.66 - 3.22: 9560 3.22 - 3.78: 14699 3.78 - 4.34: 19838 4.34 - 4.90: 33289 Nonbonded interactions: 77586 Sorted by model distance: nonbonded pdb=" OG1 THR A 81 " pdb=" OD1 ASN a 319 " model vdw 2.103 3.040 nonbonded pdb=" O ASN a 409 " pdb=" OG1 THR a 412 " model vdw 2.119 3.040 nonbonded pdb=" OG SER b 367 " pdb=" OH TYR b 393 " model vdw 2.120 3.040 nonbonded pdb=" OG SER B 169 " pdb=" OE1 GLN B 218 " model vdw 2.153 3.040 nonbonded pdb=" OG1 THR C 226 " pdb=" OE2 GLU C 228 " model vdw 2.227 3.040 ... (remaining 77581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 60 through 259 or resid 301 through 302)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'E' selection = chain 'N' } ncs_group { reference = (chain 'H' and resid 6 through 109) selection = chain 'L' } ncs_group { reference = (chain 'a' and (resid 260 through 267 or resid 278 through 414 or resid 701 thro \ ugh 702)) selection = (chain 'b' and (resid 260 through 267 or resid 278 through 414 or resid 701 thro \ ugh 702)) selection = (chain 'c' and (resid 260 through 267 or resid 278 through 414 or resid 701 thro \ ugh 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.940 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.260 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.005 0.054 10192 Z= 0.335 Angle : 0.965 8.940 13835 Z= 0.467 Chirality : 0.056 0.667 1757 Planarity : 0.020 0.309 1685 Dihedral : 13.788 109.016 4412 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.11 % Allowed : 1.21 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.26), residues: 971 helix: 0.21 (0.27), residues: 321 sheet: -2.19 (0.37), residues: 151 loop : -1.24 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 196 HIS 0.020 0.002 HIS b 354 PHE 0.015 0.002 PHE b 262 TYR 0.024 0.002 TYR C 253 ARG 0.017 0.002 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 THR cc_start: 0.8439 (p) cc_final: 0.7900 (p) REVERT: B 76 GLU cc_start: 0.8152 (tp30) cc_final: 0.7772 (tp30) REVERT: B 80 MET cc_start: 0.7550 (ttt) cc_final: 0.6996 (mtp) REVERT: C 76 GLU cc_start: 0.7680 (tt0) cc_final: 0.7192 (tm-30) REVERT: C 194 MET cc_start: 0.8460 (tpp) cc_final: 0.7945 (tpt) REVERT: b 283 TRP cc_start: 0.7533 (m-90) cc_final: 0.7186 (m-90) REVERT: b 371 TYR cc_start: 0.8689 (p90) cc_final: 0.8194 (p90) REVERT: c 286 ILE cc_start: 0.7288 (mm) cc_final: 0.7051 (mp) outliers start: 1 outliers final: 1 residues processed: 243 average time/residue: 0.2110 time to fit residues: 72.9601 Evaluate side-chains 215 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 395 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN C 223 GLN a 319 ASN a 335 GLN a 398 HIS b 305 HIS b 348 GLN ** b 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 305 HIS c 348 GLN c 354 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.197990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168734 restraints weight = 13176.228| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.95 r_work: 0.3901 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10192 Z= 0.343 Angle : 0.823 11.118 13835 Z= 0.378 Chirality : 0.051 0.360 1757 Planarity : 0.004 0.049 1685 Dihedral : 9.786 77.667 2507 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.97 % Allowed : 9.79 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.27), residues: 971 helix: 0.34 (0.28), residues: 334 sheet: -2.04 (0.38), residues: 152 loop : -1.12 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 196 HIS 0.006 0.001 HIS B 93 PHE 0.017 0.002 PHE c 318 TYR 0.025 0.002 TYR c 363 ARG 0.008 0.001 ARG c 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.7919 (ttt) cc_final: 0.7291 (mtp) REVERT: B 247 GLN cc_start: 0.8080 (tp40) cc_final: 0.7870 (tp40) REVERT: C 194 MET cc_start: 0.8334 (tpp) cc_final: 0.7914 (tpt) REVERT: b 321 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.6870 (mp-120) REVERT: b 357 ASP cc_start: 0.8394 (t0) cc_final: 0.8160 (t70) REVERT: b 371 TYR cc_start: 0.8748 (p90) cc_final: 0.8324 (p90) REVERT: c 286 ILE cc_start: 0.7488 (mm) cc_final: 0.7269 (mp) outliers start: 27 outliers final: 19 residues processed: 230 average time/residue: 0.2102 time to fit residues: 68.3909 Evaluate side-chains 218 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 348 GLN Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 367 SER Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 398 HIS Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 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 = 0.4339 r_free = 0.4339 target = 0.200938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171694 restraints weight = 13289.501| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.01 r_work: 0.3924 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10192 Z= 0.189 Angle : 0.676 9.598 13835 Z= 0.315 Chirality : 0.044 0.332 1757 Planarity : 0.004 0.045 1685 Dihedral : 8.573 59.467 2507 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.42 % Allowed : 13.64 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.27), residues: 971 helix: 0.72 (0.29), residues: 328 sheet: -2.05 (0.39), residues: 143 loop : -1.05 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 196 HIS 0.005 0.001 HIS A 115 PHE 0.012 0.001 PHE c 318 TYR 0.025 0.001 TYR c 363 ARG 0.007 0.001 ARG c 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 GLU cc_start: 0.8153 (tp30) cc_final: 0.7770 (tp30) REVERT: B 247 GLN cc_start: 0.8152 (tp40) cc_final: 0.7855 (tp40) REVERT: C 194 MET cc_start: 0.8307 (tpp) cc_final: 0.7892 (tpt) REVERT: b 371 TYR cc_start: 0.8725 (p90) cc_final: 0.8217 (p90) REVERT: c 307 GLU cc_start: 0.5778 (tm-30) cc_final: 0.5562 (tm-30) REVERT: c 353 ASN cc_start: 0.7923 (m110) cc_final: 0.7563 (m110) outliers start: 22 outliers final: 16 residues processed: 237 average time/residue: 0.2092 time to fit residues: 70.6687 Evaluate side-chains 229 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 398 HIS Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.0370 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 335 GLN ** b 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.194925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.165800 restraints weight = 13266.437| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.96 r_work: 0.3870 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10192 Z= 0.283 Angle : 0.693 9.657 13835 Z= 0.325 Chirality : 0.046 0.366 1757 Planarity : 0.004 0.051 1685 Dihedral : 7.985 57.085 2507 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.07 % Allowed : 14.19 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.27), residues: 971 helix: 0.77 (0.29), residues: 328 sheet: -2.03 (0.39), residues: 143 loop : -0.95 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 196 HIS 0.005 0.001 HIS B 93 PHE 0.012 0.002 PHE a 309 TYR 0.024 0.002 TYR c 363 ARG 0.008 0.001 ARG c 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.8993 (mm) cc_final: 0.8776 (pt) REVERT: B 247 GLN cc_start: 0.8210 (tp40) cc_final: 0.7324 (tp40) REVERT: C 194 MET cc_start: 0.8377 (tpp) cc_final: 0.7927 (tpt) REVERT: b 321 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.6605 (mp-120) REVERT: b 371 TYR cc_start: 0.8808 (p90) cc_final: 0.8228 (p90) REVERT: c 308 GLU cc_start: 0.7626 (mp0) cc_final: 0.7287 (mp0) REVERT: c 351 MET cc_start: 0.8914 (tpt) cc_final: 0.8390 (tpp) REVERT: c 353 ASN cc_start: 0.7993 (m110) cc_final: 0.7663 (m110) REVERT: c 410 MET cc_start: 0.6910 (ttt) cc_final: 0.6704 (ttm) outliers start: 37 outliers final: 27 residues processed: 229 average time/residue: 0.2150 time to fit residues: 69.5224 Evaluate side-chains 231 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 395 ASN Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 78 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 chunk 73 optimal weight: 8.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.193442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.164591 restraints weight = 13382.603| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.96 r_work: 0.3861 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10192 Z= 0.282 Angle : 0.694 9.640 13835 Z= 0.326 Chirality : 0.045 0.372 1757 Planarity : 0.004 0.052 1685 Dihedral : 7.776 56.570 2507 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.29 % Allowed : 15.62 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.27), residues: 971 helix: 0.77 (0.29), residues: 328 sheet: -2.02 (0.38), residues: 157 loop : -0.89 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 196 HIS 0.004 0.001 HIS B 93 PHE 0.011 0.002 PHE c 318 TYR 0.017 0.001 TYR c 363 ARG 0.007 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 247 GLN cc_start: 0.8170 (tp40) cc_final: 0.7749 (tp40) REVERT: B 248 ARG cc_start: 0.8198 (ttm110) cc_final: 0.7987 (ttm110) REVERT: C 194 MET cc_start: 0.8401 (tpp) cc_final: 0.7918 (tpt) REVERT: b 321 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.6602 (mp-120) REVERT: b 371 TYR cc_start: 0.8844 (p90) cc_final: 0.8189 (p90) REVERT: c 353 ASN cc_start: 0.8001 (m110) cc_final: 0.7694 (m110) outliers start: 39 outliers final: 27 residues processed: 224 average time/residue: 0.2116 time to fit residues: 66.9728 Evaluate side-chains 229 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 395 ASN Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 367 SER Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN a 405 GLN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.194023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165433 restraints weight = 13336.181| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.96 r_work: 0.3870 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10192 Z= 0.242 Angle : 0.668 9.618 13835 Z= 0.315 Chirality : 0.044 0.362 1757 Planarity : 0.004 0.049 1685 Dihedral : 7.591 56.378 2507 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.73 % Allowed : 17.16 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 971 helix: 0.87 (0.29), residues: 328 sheet: -1.92 (0.38), residues: 157 loop : -0.86 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 196 HIS 0.004 0.001 HIS b 354 PHE 0.010 0.001 PHE c 318 TYR 0.028 0.001 TYR c 363 ARG 0.007 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.9035 (mm) cc_final: 0.8637 (pt) REVERT: B 247 GLN cc_start: 0.8161 (tp40) cc_final: 0.7745 (tp40) REVERT: C 194 MET cc_start: 0.8411 (tpp) cc_final: 0.7946 (tpt) REVERT: b 321 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.6430 (mp-120) REVERT: b 371 TYR cc_start: 0.8816 (p90) cc_final: 0.8091 (p90) REVERT: c 351 MET cc_start: 0.8822 (tpt) cc_final: 0.8375 (tpp) REVERT: c 353 ASN cc_start: 0.7993 (m110) cc_final: 0.7642 (m110) REVERT: c 410 MET cc_start: 0.7038 (ttm) cc_final: 0.6824 (ttt) outliers start: 43 outliers final: 32 residues processed: 228 average time/residue: 0.2190 time to fit residues: 71.4953 Evaluate side-chains 235 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 395 ASN Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 348 GLN Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 0.0000 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 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 = 0.4295 r_free = 0.4295 target = 0.195727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.166749 restraints weight = 13523.194| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.02 r_work: 0.3893 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10192 Z= 0.194 Angle : 0.650 9.587 13835 Z= 0.306 Chirality : 0.043 0.351 1757 Planarity : 0.004 0.102 1685 Dihedral : 7.433 56.093 2507 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.85 % Allowed : 18.59 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.28), residues: 971 helix: 0.95 (0.29), residues: 328 sheet: -1.83 (0.39), residues: 157 loop : -0.87 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 196 HIS 0.005 0.001 HIS B 124 PHE 0.011 0.001 PHE b 316 TYR 0.025 0.001 TYR c 363 ARG 0.009 0.001 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.6300 (m-80) cc_final: 0.6038 (m-80) REVERT: B 76 GLU cc_start: 0.8168 (tp30) cc_final: 0.7708 (tp30) REVERT: B 247 GLN cc_start: 0.8126 (tp40) cc_final: 0.7702 (tp40) REVERT: C 194 MET cc_start: 0.8389 (tpp) cc_final: 0.7940 (tpt) REVERT: b 321 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.6230 (mp-120) REVERT: b 371 TYR cc_start: 0.8817 (p90) cc_final: 0.8055 (p90) REVERT: c 351 MET cc_start: 0.8832 (tpt) cc_final: 0.8229 (tpp) REVERT: c 353 ASN cc_start: 0.7968 (m110) cc_final: 0.7706 (m110) REVERT: c 410 MET cc_start: 0.7020 (ttm) cc_final: 0.6813 (ttt) outliers start: 35 outliers final: 29 residues processed: 228 average time/residue: 0.1990 time to fit residues: 65.5332 Evaluate side-chains 232 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 262 PHE Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 395 ASN Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 chunk 117 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.195093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.165934 restraints weight = 13539.458| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 3.05 r_work: 0.3885 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10192 Z= 0.218 Angle : 0.660 9.611 13835 Z= 0.310 Chirality : 0.043 0.341 1757 Planarity : 0.004 0.064 1685 Dihedral : 7.333 56.471 2507 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.40 % Allowed : 18.04 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.28), residues: 971 helix: 0.95 (0.29), residues: 328 sheet: -1.82 (0.39), residues: 157 loop : -0.87 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 196 HIS 0.004 0.001 HIS B 124 PHE 0.010 0.001 PHE b 316 TYR 0.022 0.001 TYR c 363 ARG 0.007 0.001 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.6334 (m-80) cc_final: 0.6080 (m-80) REVERT: B 76 GLU cc_start: 0.8164 (tp30) cc_final: 0.7702 (tp30) REVERT: B 247 GLN cc_start: 0.8136 (tp40) cc_final: 0.7681 (tp-100) REVERT: C 194 MET cc_start: 0.8424 (tpp) cc_final: 0.7991 (tpt) REVERT: a 338 ASN cc_start: 0.8849 (t0) cc_final: 0.8606 (t0) REVERT: a 398 HIS cc_start: 0.8023 (t70) cc_final: 0.7626 (t70) REVERT: b 321 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.6382 (mp-120) REVERT: b 371 TYR cc_start: 0.8838 (p90) cc_final: 0.8072 (p90) REVERT: c 351 MET cc_start: 0.8838 (tpt) cc_final: 0.8268 (tpp) REVERT: c 353 ASN cc_start: 0.7974 (m110) cc_final: 0.7686 (m110) REVERT: c 410 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6838 (ttt) outliers start: 40 outliers final: 31 residues processed: 224 average time/residue: 0.2081 time to fit residues: 66.3930 Evaluate side-chains 234 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 262 PHE Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 395 ASN Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 348 GLN Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 117 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.195266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.166125 restraints weight = 13439.589| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 3.04 r_work: 0.3876 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10192 Z= 0.231 Angle : 0.672 9.604 13835 Z= 0.317 Chirality : 0.044 0.335 1757 Planarity : 0.004 0.057 1685 Dihedral : 7.299 56.467 2507 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.07 % Allowed : 18.48 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.27), residues: 971 helix: 0.94 (0.29), residues: 328 sheet: -1.81 (0.39), residues: 157 loop : -0.90 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 196 HIS 0.005 0.001 HIS B 124 PHE 0.011 0.001 PHE b 316 TYR 0.035 0.002 TYR A 253 ARG 0.007 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.6287 (m-80) cc_final: 0.6078 (m-80) REVERT: B 247 GLN cc_start: 0.8119 (tp40) cc_final: 0.7677 (tp-100) REVERT: C 194 MET cc_start: 0.8419 (tpp) cc_final: 0.7995 (tpt) REVERT: a 338 ASN cc_start: 0.8863 (t0) cc_final: 0.8566 (t0) REVERT: a 398 HIS cc_start: 0.8008 (t70) cc_final: 0.7396 (t70) REVERT: b 321 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.6379 (mp-120) REVERT: b 371 TYR cc_start: 0.8836 (p90) cc_final: 0.8067 (p90) REVERT: c 351 MET cc_start: 0.8827 (tpt) cc_final: 0.8250 (tpp) REVERT: c 410 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6800 (ttt) outliers start: 37 outliers final: 30 residues processed: 222 average time/residue: 0.2035 time to fit residues: 64.8505 Evaluate side-chains 229 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 262 PHE Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.0470 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 109 optimal weight: 0.0770 chunk 104 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.196703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.167897 restraints weight = 13466.260| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.04 r_work: 0.3897 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10192 Z= 0.188 Angle : 0.656 9.572 13835 Z= 0.311 Chirality : 0.043 0.326 1757 Planarity : 0.004 0.042 1685 Dihedral : 7.200 56.084 2507 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.74 % Allowed : 18.92 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.27), residues: 971 helix: 0.97 (0.29), residues: 328 sheet: -1.78 (0.39), residues: 157 loop : -0.89 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 196 HIS 0.005 0.001 HIS B 124 PHE 0.015 0.001 PHE A 147 TYR 0.034 0.001 TYR A 253 ARG 0.007 0.001 ARG a 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.6652 (OUTLIER) cc_final: 0.6431 (t0) REVERT: B 247 GLN cc_start: 0.8144 (tp40) cc_final: 0.7715 (tp-100) REVERT: C 194 MET cc_start: 0.8406 (tpp) cc_final: 0.8024 (tpt) REVERT: a 338 ASN cc_start: 0.8842 (t0) cc_final: 0.8514 (t0) REVERT: a 398 HIS cc_start: 0.7967 (t70) cc_final: 0.7403 (t70) REVERT: b 321 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.6301 (mp-120) REVERT: b 371 TYR cc_start: 0.8813 (p90) cc_final: 0.7924 (p90) REVERT: c 351 MET cc_start: 0.8786 (tpt) cc_final: 0.8229 (tpp) REVERT: c 410 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6797 (ttt) outliers start: 34 outliers final: 29 residues processed: 221 average time/residue: 0.2014 time to fit residues: 63.5388 Evaluate side-chains 228 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 262 PHE Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 348 GLN Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 113 optimal weight: 0.0050 chunk 79 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.196578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.167834 restraints weight = 13396.108| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 3.02 r_work: 0.3895 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 10192 Z= 0.289 Angle : 1.048 59.200 13835 Z= 0.606 Chirality : 0.043 0.326 1757 Planarity : 0.005 0.150 1685 Dihedral : 7.197 56.105 2507 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.96 % Allowed : 18.92 % Favored : 77.12 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.27), residues: 971 helix: 1.00 (0.29), residues: 326 sheet: -1.77 (0.39), residues: 157 loop : -0.85 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 196 HIS 0.005 0.001 HIS B 124 PHE 0.011 0.001 PHE C 233 TYR 0.027 0.001 TYR c 363 ARG 0.006 0.001 ARG a 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4295.41 seconds wall clock time: 77 minutes 43.86 seconds (4663.86 seconds total)