Starting phenix.real_space_refine on Sat Nov 16 01:03:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck7_45643/11_2024/9ck7_45643.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck7_45643/11_2024/9ck7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck7_45643/11_2024/9ck7_45643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck7_45643/11_2024/9ck7_45643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck7_45643/11_2024/9ck7_45643.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ck7_45643/11_2024/9ck7_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.89, per 1000 atoms: 0.89 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: 3.61 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.07 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: 2.57 Time building geometry restraints manager: 3.94 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: 9.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.060 Find NCS groups from input model: 0.550 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.510 ------------------------------------------------------------------------------- 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 : 1.010 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: 0.2167 time to fit residues: 74.7519 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 : 1.101 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.7762 (ttt) cc_final: 0.7096 (mtp) REVERT: B 247 GLN cc_start: 0.8075 (tp40) cc_final: 0.7852 (tp40) REVERT: C 194 MET cc_start: 0.8356 (tpp) cc_final: 0.7921 (tpt) REVERT: b 283 TRP cc_start: 0.7637 (m-90) cc_final: 0.7412 (m-90) REVERT: b 321 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.6823 (mp-120) REVERT: b 357 ASP cc_start: 0.8436 (t0) cc_final: 0.8211 (t70) REVERT: b 371 TYR cc_start: 0.8714 (p90) cc_final: 0.8265 (p90) REVERT: c 286 ILE cc_start: 0.7417 (mm) cc_final: 0.7179 (mp) outliers start: 27 outliers final: 19 residues processed: 230 average time/residue: 0.2233 time to fit residues: 72.6122 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 : 1.115 ------------------------------------------------------------------------------- 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 61 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10192 Z= 0.239 Angle : 0.703 9.642 13835 Z= 0.328 Chirality : 0.046 0.337 1757 Planarity : 0.004 0.044 1685 Dihedral : 8.689 58.749 2507 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.64 % Allowed : 13.42 % 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: -1.00 (0.27), residues: 971 helix: 0.68 (0.29), residues: 328 sheet: -2.07 (0.38), residues: 152 loop : -1.07 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 196 HIS 0.005 0.001 HIS A 115 PHE 0.013 0.001 PHE c 318 TYR 0.025 0.001 TYR c 363 ARG 0.008 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 243 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 GLU cc_start: 0.8141 (tp30) cc_final: 0.7723 (tp30) REVERT: B 247 GLN cc_start: 0.8195 (tp40) cc_final: 0.7878 (tp40) REVERT: C 194 MET cc_start: 0.8387 (tpp) cc_final: 0.7913 (tpt) REVERT: b 283 TRP cc_start: 0.7595 (m-90) cc_final: 0.7337 (m-90) REVERT: b 371 TYR cc_start: 0.8738 (p90) cc_final: 0.8210 (p90) REVERT: c 307 GLU cc_start: 0.5871 (tm-30) cc_final: 0.5590 (tm-30) REVERT: c 353 ASN cc_start: 0.7949 (m110) cc_final: 0.7638 (m110) outliers start: 24 outliers final: 17 residues processed: 229 average time/residue: 0.2119 time to fit residues: 68.9859 Evaluate side-chains 223 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 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 108 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 319 ASN b 335 GLN ** b 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10192 Z= 0.378 Angle : 0.778 9.735 13835 Z= 0.364 Chirality : 0.049 0.385 1757 Planarity : 0.004 0.043 1685 Dihedral : 8.328 57.525 2507 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.40 % Allowed : 14.19 % Favored : 81.41 % 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: -1.00 (0.27), residues: 971 helix: 0.62 (0.29), residues: 328 sheet: -2.19 (0.38), residues: 160 loop : -0.95 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 196 HIS 0.006 0.002 HIS B 141 PHE 0.016 0.002 PHE a 309 TYR 0.026 0.002 TYR c 363 ARG 0.009 0.001 ARG c 314 *********************** 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 253 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.9034 (mm) cc_final: 0.8779 (pt) REVERT: B 120 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8200 (tt) REVERT: B 247 GLN cc_start: 0.8234 (tp40) cc_final: 0.7324 (tp40) REVERT: C 194 MET cc_start: 0.8422 (tpp) cc_final: 0.7895 (tpt) REVERT: a 379 ARG cc_start: 0.7176 (ttp80) cc_final: 0.6922 (ttp80) REVERT: b 321 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.6624 (mp-120) REVERT: b 357 ASP cc_start: 0.8491 (t0) cc_final: 0.8252 (t70) REVERT: b 371 TYR cc_start: 0.8867 (p90) cc_final: 0.8251 (p90) REVERT: c 351 MET cc_start: 0.8946 (tpt) cc_final: 0.8422 (tpp) REVERT: c 353 ASN cc_start: 0.8040 (m110) cc_final: 0.7635 (m110) outliers start: 40 outliers final: 28 residues processed: 233 average time/residue: 0.2094 time to fit residues: 69.0273 Evaluate side-chains 235 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain B residue 200 TYR 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 292 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 265 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** c 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2667 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= 0.271 Angle : 0.690 9.647 13835 Z= 0.324 Chirality : 0.045 0.372 1757 Planarity : 0.004 0.043 1685 Dihedral : 7.961 56.107 2507 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.40 % Allowed : 16.72 % Favored : 78.88 % 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: -0.85 (0.27), residues: 971 helix: 0.77 (0.29), residues: 328 sheet: -2.06 (0.38), residues: 152 loop : -0.93 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 196 HIS 0.005 0.001 HIS B 124 PHE 0.011 0.001 PHE c 318 TYR 0.020 0.001 TYR c 363 ARG 0.009 0.001 ARG c 325 *********************** 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 246 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8198 (ptt-90) cc_final: 0.7953 (ptt180) REVERT: B 247 GLN cc_start: 0.8184 (tp40) cc_final: 0.7932 (tp40) REVERT: C 194 MET cc_start: 0.8409 (tpp) cc_final: 0.7929 (tpt) REVERT: a 338 ASN cc_start: 0.8867 (t0) cc_final: 0.8665 (t0) REVERT: b 321 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.6581 (mp-120) REVERT: b 371 TYR cc_start: 0.8841 (p90) cc_final: 0.8158 (p90) REVERT: c 353 ASN cc_start: 0.7960 (m110) cc_final: 0.7581 (m110) outliers start: 40 outliers final: 28 residues processed: 228 average time/residue: 0.2123 time to fit residues: 68.7153 Evaluate side-chains 232 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 200 TYR 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 292 CYS 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 405 GLN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10192 Z= 0.216 Angle : 0.664 9.597 13835 Z= 0.313 Chirality : 0.044 0.363 1757 Planarity : 0.004 0.041 1685 Dihedral : 7.751 56.190 2507 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.07 % Allowed : 17.93 % Favored : 78.00 % 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: -0.76 (0.27), residues: 971 helix: 0.88 (0.29), residues: 328 sheet: -1.94 (0.39), residues: 152 loop : -0.93 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 196 HIS 0.004 0.001 HIS B 124 PHE 0.010 0.001 PHE C 233 TYR 0.030 0.001 TYR c 363 ARG 0.009 0.001 ARG c 325 *********************** 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 248 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 247 GLN cc_start: 0.8140 (tp40) cc_final: 0.7714 (tp40) REVERT: C 194 MET cc_start: 0.8391 (tpp) cc_final: 0.7875 (tpt) REVERT: b 321 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6499 (mp-120) REVERT: b 357 ASP cc_start: 0.8399 (t0) cc_final: 0.8143 (t70) REVERT: b 371 TYR cc_start: 0.8822 (p90) cc_final: 0.8060 (p90) REVERT: c 351 MET cc_start: 0.8849 (tpt) cc_final: 0.8308 (tpp) REVERT: c 353 ASN cc_start: 0.7972 (m110) cc_final: 0.7639 (m110) REVERT: c 410 MET cc_start: 0.6992 (ttm) cc_final: 0.6724 (ttt) outliers start: 37 outliers final: 28 residues processed: 232 average time/residue: 0.2035 time to fit residues: 67.3107 Evaluate side-chains 229 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain B residue 200 TYR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.0010 chunk 66 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 116 optimal weight: 0.0970 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 319 ASN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN c 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10192 Z= 0.200 Angle : 0.657 9.798 13835 Z= 0.308 Chirality : 0.043 0.350 1757 Planarity : 0.003 0.045 1685 Dihedral : 7.518 56.226 2507 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.07 % Allowed : 18.92 % Favored : 77.01 % 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 (0.28), residues: 971 helix: 0.95 (0.29), residues: 328 sheet: -1.87 (0.38), residues: 166 loop : -0.92 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 196 HIS 0.004 0.001 HIS B 124 PHE 0.010 0.001 PHE C 233 TYR 0.025 0.001 TYR c 363 ARG 0.008 0.001 ARG C 193 *********************** 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 242 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8161 (ptt-90) cc_final: 0.7916 (ptt180) REVERT: B 125 LYS cc_start: 0.8531 (tptp) cc_final: 0.8073 (ttmm) REVERT: B 247 GLN cc_start: 0.8124 (tp40) cc_final: 0.7727 (tp40) REVERT: C 194 MET cc_start: 0.8418 (tpp) cc_final: 0.7948 (tpt) REVERT: a 338 ASN cc_start: 0.8853 (t0) cc_final: 0.8585 (t0) REVERT: a 398 HIS cc_start: 0.7955 (t70) cc_final: 0.7610 (t70) REVERT: b 321 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.6351 (mp-120) REVERT: b 371 TYR cc_start: 0.8817 (p90) cc_final: 0.8022 (p90) REVERT: c 351 MET cc_start: 0.8844 (tpt) cc_final: 0.8219 (tpp) REVERT: c 353 ASN cc_start: 0.7941 (m110) cc_final: 0.7543 (m110) REVERT: c 410 MET cc_start: 0.7052 (ttm) cc_final: 0.6778 (ttt) outliers start: 37 outliers final: 28 residues processed: 227 average time/residue: 0.2041 time to fit residues: 66.6316 Evaluate side-chains 231 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 212 CYS 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 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 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10192 Z= 0.377 Angle : 0.771 9.706 13835 Z= 0.363 Chirality : 0.047 0.357 1757 Planarity : 0.004 0.043 1685 Dihedral : 7.912 58.133 2507 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.07 % Allowed : 19.36 % Favored : 76.57 % 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: -0.87 (0.27), residues: 971 helix: 0.73 (0.29), residues: 327 sheet: -1.97 (0.40), residues: 143 loop : -0.99 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 196 HIS 0.005 0.001 HIS B 141 PHE 0.013 0.002 PHE a 309 TYR 0.020 0.002 TYR c 363 ARG 0.008 0.001 ARG C 193 *********************** 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 236 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 247 GLN cc_start: 0.8235 (tp40) cc_final: 0.7809 (tp40) REVERT: C 194 MET cc_start: 0.8444 (tpp) cc_final: 0.7999 (tpt) REVERT: a 338 ASN cc_start: 0.8853 (t0) cc_final: 0.8596 (t0) REVERT: a 398 HIS cc_start: 0.7958 (t70) cc_final: 0.7359 (t70) REVERT: b 321 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.6646 (mp-120) REVERT: c 351 MET cc_start: 0.9035 (tpt) cc_final: 0.8456 (tpp) REVERT: c 410 MET cc_start: 0.7133 (ttm) cc_final: 0.6723 (ttt) outliers start: 37 outliers final: 26 residues processed: 220 average time/residue: 0.2139 time to fit residues: 67.5526 Evaluate side-chains 223 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 200 TYR 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 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 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3060 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= 0.209 Angle : 0.681 9.600 13835 Z= 0.322 Chirality : 0.043 0.336 1757 Planarity : 0.003 0.041 1685 Dihedral : 7.623 55.781 2507 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.52 % Allowed : 20.46 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 971 helix: 0.86 (0.29), residues: 328 sheet: -1.92 (0.39), residues: 152 loop : -0.95 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 196 HIS 0.004 0.001 HIS B 124 PHE 0.011 0.001 PHE b 316 TYR 0.032 0.001 TYR c 363 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 233 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LYS cc_start: 0.8541 (tptp) cc_final: 0.8094 (ttmm) REVERT: B 247 GLN cc_start: 0.8156 (tp40) cc_final: 0.7757 (tp40) REVERT: C 194 MET cc_start: 0.8425 (tpp) cc_final: 0.7982 (tpt) REVERT: a 338 ASN cc_start: 0.8846 (t0) cc_final: 0.8543 (t0) REVERT: a 398 HIS cc_start: 0.7906 (t70) cc_final: 0.7414 (t70) REVERT: b 321 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6416 (mp-120) REVERT: c 351 MET cc_start: 0.8901 (tpt) cc_final: 0.8336 (tpp) REVERT: c 410 MET cc_start: 0.7069 (ttm) cc_final: 0.6728 (ttt) outliers start: 32 outliers final: 29 residues processed: 220 average time/residue: 0.2330 time to fit residues: 73.8786 Evaluate side-chains 223 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 B residue 200 TYR 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 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 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 326 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10192 Z= 0.386 Angle : 0.781 9.716 13835 Z= 0.368 Chirality : 0.048 0.355 1757 Planarity : 0.004 0.042 1685 Dihedral : 7.792 57.657 2507 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.41 % Allowed : 20.90 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.27), residues: 971 helix: 0.62 (0.29), residues: 328 sheet: -2.09 (0.40), residues: 143 loop : -1.06 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 196 HIS 0.005 0.001 HIS A 179 PHE 0.012 0.002 PHE b 316 TYR 0.028 0.002 TYR c 363 ARG 0.008 0.001 ARG c 314 ********************** 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 228 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 TYR cc_start: 0.7397 (m-80) cc_final: 0.7038 (m-80) REVERT: C 100 GLU cc_start: 0.7446 (pm20) cc_final: 0.7187 (pm20) REVERT: C 194 MET cc_start: 0.8454 (tpp) cc_final: 0.8006 (tpt) REVERT: a 304 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8357 (mtpp) REVERT: a 338 ASN cc_start: 0.8859 (t0) cc_final: 0.8553 (t0) REVERT: a 398 HIS cc_start: 0.7948 (t70) cc_final: 0.7422 (t70) REVERT: b 282 ARG cc_start: 0.7803 (tpp80) cc_final: 0.7425 (tpp80) REVERT: b 321 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.6647 (mp-120) REVERT: c 351 MET cc_start: 0.8985 (tpt) cc_final: 0.8431 (tpp) REVERT: c 410 MET cc_start: 0.7128 (ttm) cc_final: 0.6729 (ttt) outliers start: 31 outliers final: 26 residues processed: 216 average time/residue: 0.2062 time to fit residues: 63.5027 Evaluate side-chains 224 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 200 TYR 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 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 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 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.193138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.164789 restraints weight = 13402.971| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.97 r_work: 0.3866 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10192 Z= 0.222 Angle : 0.700 9.595 13835 Z= 0.333 Chirality : 0.043 0.322 1757 Planarity : 0.004 0.040 1685 Dihedral : 7.523 55.858 2507 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.07 % Allowed : 20.35 % Favored : 75.58 % 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: -0.93 (0.27), residues: 971 helix: 0.78 (0.29), residues: 328 sheet: -2.13 (0.37), residues: 166 loop : -0.97 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 196 HIS 0.007 0.001 HIS A 179 PHE 0.011 0.001 PHE b 316 TYR 0.030 0.001 TYR c 363 ARG 0.007 0.001 ARG a 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2408.46 seconds wall clock time: 45 minutes 8.08 seconds (2708.08 seconds total)