Starting phenix.real_space_refine on Fri Jan 17 03:28:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve8_43168/01_2025/8ve8_43168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve8_43168/01_2025/8ve8_43168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ve8_43168/01_2025/8ve8_43168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve8_43168/01_2025/8ve8_43168.map" model { file = "/net/cci-nas-00/data/ceres_data/8ve8_43168/01_2025/8ve8_43168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve8_43168/01_2025/8ve8_43168.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 87 5.16 5 C 6418 2.51 5 N 1682 2.21 5 O 2140 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-5571/modules/chem_data/mon_lib" Total number of atoms: 10327 Number of models: 1 Model: "" Number of chains: 34 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: "a" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "b" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "c" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 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: "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: 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: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" 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: "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: 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" 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: "X" 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: "Y" 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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 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: 8.40, per 1000 atoms: 0.81 Number of scatterers: 10327 At special positions: 0 Unit cell: (94.058, 101.956, 125.65, 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 87 16.00 O 2140 8.00 N 1682 7.00 C 6418 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=1.29 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=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 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=2.08 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=1.63 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=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " 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 K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG O 1 " - " FUC O 3 " " NAG S 1 " - " FUC S 3 " " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG A 302 " - " ASN A 119 " " NAG B 301 " - " ASN B 99 " " NAG C 301 " - " ASN C 119 " " NAG C 302 " - " ASN C 99 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 109 " " NAG G 1 " - " ASN A 167 " " NAG I 1 " - " ASN A 224 " " NAG J 1 " - " ASN B 109 " " NAG K 1 " - " ASN B 224 " " NAG M 1 " - " ASN B 79 " " NAG N 1 " - " ASN B 89 " " NAG O 1 " - " ASN B 119 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN C 79 " " NAG R 1 " - " ASN C 89 " " NAG S 1 " - " ASN C 109 " " NAG T 1 " - " ASN C 167 " " NAG U 1 " - " ASN C 224 " " NAG V 1 " - " ASN a 365 " " NAG W 1 " - " ASN b 365 " " NAG X 1 " - " ASN b 395 " " NAG Y 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 373 " " 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: 3.24 Conformation dependent library (CDL) restraints added in 1.2 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 18 sheets defined 41.6% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 74 through 81 removed outlier: 3.832A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.843A pdb=" N LYS A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.739A pdb=" N ARG A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.663A pdb=" N LEU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.633A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.532A pdb=" N ALA B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.973A pdb=" N LYS B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.851A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.894A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.827A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.750A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.935A pdb=" N ILE C 201 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'a' and resid 294 through 300 removed outlier: 3.899A pdb=" N LYS a 300 " --> pdb=" O THR a 296 " (cutoff:3.500A) Processing helix chain 'a' and resid 301 through 303 No H-bonds generated for 'chain 'a' and resid 301 through 303' Processing helix chain 'a' and resid 307 through 326 removed outlier: 3.505A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 345 removed outlier: 3.730A pdb=" N LYS a 339 " --> pdb=" O GLN a 335 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.523A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 413 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 removed outlier: 3.507A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.949A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.559A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 413 Processing helix chain 'c' and resid 281 through 285 removed outlier: 3.520A pdb=" N LEU c 285 " --> pdb=" O ARG c 282 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 removed outlier: 3.507A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.994A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU c 344 " --> pdb=" O ALA c 340 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.560A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 412 removed outlier: 3.943A pdb=" N THR c 412 " --> pdb=" O ASP c 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 83 through 86 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.805A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 155 removed outlier: 5.486A pdb=" N THR B 87 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG B 235 " --> pdb=" O THR B 87 " (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 83 through 87 Processing sheet with id=AA7, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AA8, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB1, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.286A pdb=" N UNK L 17 " --> pdb=" O UNK L 77 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N UNK L 77 " --> pdb=" O UNK L 17 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AB6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.575A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 2 through 6 removed outlier: 6.406A pdb=" N UNK H 76 " --> pdb=" O UNK H 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.768A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N UNK H 96 " --> pdb=" O UNK H 100D" (cutoff:3.500A) removed outlier: 5.688A pdb=" N UNK H 100D" --> pdb=" O UNK H 96 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.768A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3085 1.34 - 1.47: 2876 1.47 - 1.61: 4412 1.61 - 1.74: 0 1.74 - 1.87: 132 Bond restraints: 10505 Sorted by residual: bond pdb=" N ILE C 213 " pdb=" CA ILE C 213 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.19e-02 7.06e+03 1.38e+01 bond pdb=" C PRO C 83 " pdb=" O PRO C 83 " ideal model delta sigma weight residual 1.233 1.202 0.031 1.10e-02 8.26e+03 7.85e+00 bond pdb=" N CYS C 212 " pdb=" CA CYS C 212 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.10e-02 8.26e+03 7.56e+00 bond pdb=" N TRP A 227 " pdb=" CA TRP A 227 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.30e-02 5.92e+03 7.46e+00 bond pdb=" N TYR b 366 " pdb=" CA TYR b 366 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.18e+00 ... (remaining 10500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 12952 1.47 - 2.95: 1049 2.95 - 4.42: 225 4.42 - 5.89: 41 5.89 - 7.37: 7 Bond angle restraints: 14274 Sorted by residual: angle pdb=" N CYS A 231 " pdb=" CA CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sigma weight residual 109.94 116.30 -6.36 1.60e+00 3.91e-01 1.58e+01 angle pdb=" CA GLU A 228 " pdb=" C GLU A 228 " pdb=" O GLU A 228 " ideal model delta sigma weight residual 121.23 117.01 4.22 1.07e+00 8.73e-01 1.56e+01 angle pdb=" CA ASN c 365 " pdb=" CB ASN c 365 " pdb=" CG ASN c 365 " ideal model delta sigma weight residual 112.60 116.54 -3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" N ASN a 365 " pdb=" CA ASN a 365 " pdb=" C ASN a 365 " ideal model delta sigma weight residual 112.92 108.08 4.84 1.23e+00 6.61e-01 1.55e+01 angle pdb=" N PHE A 233 " pdb=" CA PHE A 233 " pdb=" C PHE A 233 " ideal model delta sigma weight residual 113.55 108.61 4.94 1.26e+00 6.30e-01 1.54e+01 ... (remaining 14269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 6844 21.15 - 42.29: 204 42.29 - 63.44: 54 63.44 - 84.59: 42 84.59 - 105.74: 21 Dihedral angle restraints: 7165 sinusoidal: 3465 harmonic: 3700 Sorted by residual: 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 -148.40 62.40 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual 93.00 142.14 -49.14 1 1.00e+01 1.00e-02 3.32e+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 46.73 46.27 1 1.00e+01 1.00e-02 2.96e+01 ... (remaining 7162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1731 0.088 - 0.177: 88 0.177 - 0.265: 13 0.265 - 0.353: 0 0.353 - 0.441: 1 Chirality restraints: 1833 Sorted by residual: chirality pdb=" C1 MAN N 5 " pdb=" O2 MAN N 4 " pdb=" C2 MAN N 5 " pdb=" O5 MAN N 5 " both_signs ideal model delta sigma weight residual False 2.40 1.96 0.44 2.00e-02 2.50e+03 4.87e+02 chirality pdb=" C1 MAN N 4 " pdb=" O3 BMA N 3 " pdb=" C2 MAN N 4 " pdb=" O5 MAN N 4 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 7.13e+01 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.77e+01 ... (remaining 1830 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.237 2.00e-02 2.50e+03 1.97e-01 4.86e+02 pdb=" C7 NAG N 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.326 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 701 " -0.117 2.00e-02 2.50e+03 9.67e-02 1.17e+02 pdb=" C7 NAG a 701 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG a 701 " -0.087 2.00e-02 2.50e+03 pdb=" N2 NAG a 701 " 0.157 2.00e-02 2.50e+03 pdb=" O7 NAG a 701 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.114 2.00e-02 2.50e+03 9.49e-02 1.13e+02 pdb=" C7 NAG Y 1 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.085 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.154 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.016 2.00e-02 2.50e+03 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 452 2.73 - 3.27: 10155 3.27 - 3.81: 16591 3.81 - 4.36: 21142 4.36 - 4.90: 35540 Nonbonded interactions: 83880 Sorted by model distance: nonbonded pdb=" OH TYR C 62 " pdb=" OE2 GLU c 396 " model vdw 2.184 3.040 nonbonded pdb=" O ALA C 195 " pdb=" OG SER C 199 " model vdw 2.198 3.040 nonbonded pdb=" O ALA B 195 " pdb=" OG SER B 199 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR B 81 " pdb=" OD1 ASN b 319 " model vdw 2.220 3.040 nonbonded pdb=" ND2 ASN B 148 " pdb=" OD1 ASN C 127 " model vdw 2.252 3.120 ... (remaining 83875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 60 through 259 or resid 301)) selection = chain 'B' selection = (chain 'C' and (resid 60 through 259 or resid 301)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) } ncs_group { reference = (chain 'H' and resid 15 through 113) selection = chain 'L' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = (chain 'a' and (resid 260 through 413 or resid 701 through 702)) selection = chain 'b' selection = (chain 'c' and (resid 260 through 413 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.380 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.990 Find NCS groups from input model: 0.560 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:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10505 Z= 0.338 Angle : 0.922 7.368 14274 Z= 0.496 Chirality : 0.047 0.441 1833 Planarity : 0.009 0.197 1734 Dihedral : 13.863 105.737 4702 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.04 (0.26), residues: 1017 helix: 0.29 (0.29), residues: 330 sheet: 0.02 (0.46), residues: 120 loop : -0.13 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.007 0.002 HIS A 93 PHE 0.014 0.002 PHE B 157 TYR 0.018 0.002 TYR B 66 ARG 0.006 0.001 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: B 134 MET cc_start: 0.8972 (tpp) cc_final: 0.8554 (tpt) REVERT: C 256 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.6957 (mtp85) REVERT: a 270 GLU cc_start: 0.6135 (mm-30) cc_final: 0.4068 (tm-30) REVERT: a 282 ARG cc_start: 0.8093 (ttp-110) cc_final: 0.7812 (ttp-170) REVERT: a 401 ASP cc_start: 0.8924 (m-30) cc_final: 0.8652 (m-30) REVERT: b 379 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7500 (ttp-110) REVERT: c 379 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7668 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 1.4013 time to fit residues: 303.2779 Evaluate side-chains 166 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 111 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 247 GLN B 92 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN C 92 HIS C 209 ASN C 247 GLN b 295 ASN b 321 GLN c 354 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.148725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130663 restraints weight = 11258.238| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.66 r_work: 0.3325 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10505 Z= 0.222 Angle : 0.596 6.517 14274 Z= 0.297 Chirality : 0.040 0.167 1833 Planarity : 0.004 0.045 1734 Dihedral : 9.245 78.730 2743 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.94 % Allowed : 6.67 % Favored : 91.40 % 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: 0.22 (0.26), residues: 1017 helix: 0.32 (0.28), residues: 336 sheet: 0.25 (0.43), residues: 138 loop : 0.15 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 210 HIS 0.006 0.001 HIS A 230 PHE 0.008 0.001 PHE b 399 TYR 0.011 0.002 TYR c 393 ARG 0.006 0.001 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8097 (mttt) REVERT: C 192 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7866 (ptm) REVERT: C 256 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.6743 (mtp180) REVERT: a 282 ARG cc_start: 0.8508 (ttp-110) cc_final: 0.8021 (ttp-170) REVERT: a 332 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7635 (ttt) REVERT: c 339 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8448 (ptmm) REVERT: c 379 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7291 (ttp-110) outliers start: 18 outliers final: 9 residues processed: 173 average time/residue: 1.4992 time to fit residues: 275.8411 Evaluate side-chains 171 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 367 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 119 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** B 230 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 = 0.3634 r_free = 0.3634 target = 0.147148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128664 restraints weight = 11260.223| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.73 r_work: 0.3281 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10505 Z= 0.186 Angle : 0.541 7.221 14274 Z= 0.271 Chirality : 0.038 0.168 1833 Planarity : 0.003 0.050 1734 Dihedral : 7.088 66.609 2743 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.15 % Allowed : 8.28 % Favored : 89.57 % 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: 0.37 (0.26), residues: 1017 helix: 0.48 (0.28), residues: 336 sheet: 0.41 (0.43), residues: 138 loop : 0.19 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.005 0.001 HIS C 230 PHE 0.008 0.001 PHE b 399 TYR 0.010 0.001 TYR C 129 ARG 0.007 0.000 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8808 (p0) cc_final: 0.8544 (p0) REVERT: B 134 MET cc_start: 0.9249 (tpp) cc_final: 0.8765 (tpt) REVERT: C 256 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.6689 (mtp85) REVERT: a 270 GLU cc_start: 0.5854 (mm-30) cc_final: 0.3611 (tm-30) REVERT: a 282 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.7973 (ttp-170) REVERT: a 332 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7771 (ttt) REVERT: c 339 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8512 (ptmm) REVERT: c 379 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7210 (ttp-110) outliers start: 20 outliers final: 7 residues processed: 178 average time/residue: 1.5103 time to fit residues: 286.2012 Evaluate side-chains 168 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 367 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 chunk 75 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 230 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 = 0.3604 r_free = 0.3604 target = 0.145123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126794 restraints weight = 11238.264| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.74 r_work: 0.3247 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10505 Z= 0.172 Angle : 0.518 7.308 14274 Z= 0.260 Chirality : 0.038 0.194 1833 Planarity : 0.003 0.042 1734 Dihedral : 6.190 58.605 2743 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.26 % Allowed : 9.25 % Favored : 88.49 % 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: 0.44 (0.27), residues: 1017 helix: 0.61 (0.29), residues: 336 sheet: 0.41 (0.43), residues: 138 loop : 0.20 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 210 HIS 0.004 0.001 HIS A 115 PHE 0.008 0.001 PHE b 399 TYR 0.015 0.001 TYR A 66 ARG 0.006 0.000 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8784 (p0) cc_final: 0.8519 (p0) REVERT: A 116 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7903 (mttt) REVERT: B 134 MET cc_start: 0.9222 (tpp) cc_final: 0.8743 (tpt) REVERT: C 95 ILE cc_start: 0.8817 (mt) cc_final: 0.8616 (tt) REVERT: C 256 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.6694 (mtp85) REVERT: a 270 GLU cc_start: 0.5874 (mm-30) cc_final: 0.3526 (tm-30) REVERT: a 282 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.7940 (ttp-170) REVERT: a 332 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7829 (ttt) REVERT: b 379 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7811 (ttp-110) REVERT: c 379 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7250 (ttp-110) REVERT: c 396 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7377 (tt0) outliers start: 21 outliers final: 10 residues processed: 180 average time/residue: 1.4614 time to fit residues: 280.3900 Evaluate side-chains 177 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 396 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 87 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 230 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 = 0.3595 r_free = 0.3595 target = 0.144477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125850 restraints weight = 11204.553| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.77 r_work: 0.3237 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10505 Z= 0.180 Angle : 0.517 7.439 14274 Z= 0.259 Chirality : 0.038 0.199 1833 Planarity : 0.003 0.041 1734 Dihedral : 6.028 55.821 2743 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.01 % Allowed : 8.82 % Favored : 88.17 % 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: 0.50 (0.27), residues: 1017 helix: 0.68 (0.29), residues: 336 sheet: 0.47 (0.43), residues: 138 loop : 0.21 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.004 0.001 HIS A 115 PHE 0.008 0.001 PHE b 399 TYR 0.009 0.001 TYR B 200 ARG 0.007 0.000 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8772 (p0) cc_final: 0.8508 (p0) REVERT: A 116 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7894 (mttt) REVERT: A 125 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8246 (tptp) REVERT: B 134 MET cc_start: 0.9222 (tpp) cc_final: 0.8751 (tpt) REVERT: C 95 ILE cc_start: 0.8848 (mt) cc_final: 0.8612 (tt) REVERT: C 256 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.6682 (mtp85) REVERT: a 270 GLU cc_start: 0.5872 (mm-30) cc_final: 0.3519 (tm-30) REVERT: a 282 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.7922 (ttp-170) REVERT: a 332 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7836 (ttt) REVERT: b 379 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7810 (ttp-110) REVERT: c 379 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7227 (ttp-110) REVERT: c 396 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7441 (tt0) outliers start: 28 outliers final: 14 residues processed: 179 average time/residue: 1.4481 time to fit residues: 276.2736 Evaluate side-chains 179 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 396 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 27 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 179 HIS ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN a 335 GLN a 354 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.139544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120853 restraints weight = 11448.495| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.77 r_work: 0.3200 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10505 Z= 0.378 Angle : 0.652 8.199 14274 Z= 0.319 Chirality : 0.043 0.208 1833 Planarity : 0.004 0.045 1734 Dihedral : 6.756 60.343 2743 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.44 % Allowed : 8.60 % Favored : 87.96 % 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: 0.12 (0.26), residues: 1017 helix: 0.24 (0.28), residues: 342 sheet: 0.42 (0.43), residues: 138 loop : 0.01 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP a 386 HIS 0.007 0.001 HIS C 230 PHE 0.013 0.002 PHE b 399 TYR 0.012 0.002 TYR B 66 ARG 0.007 0.001 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8811 (p0) cc_final: 0.8552 (p0) REVERT: A 116 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7938 (mttt) REVERT: A 125 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8297 (tptp) REVERT: B 134 MET cc_start: 0.9275 (tpp) cc_final: 0.8843 (tpt) REVERT: C 114 ASN cc_start: 0.8257 (p0) cc_final: 0.7649 (t160) REVERT: C 256 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.6824 (mtp85) REVERT: a 270 GLU cc_start: 0.5958 (mm-30) cc_final: 0.3501 (tm-30) REVERT: a 282 ARG cc_start: 0.8506 (ttp-110) cc_final: 0.7913 (ttp-170) REVERT: a 332 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7846 (ttt) REVERT: c 303 GLU cc_start: 0.8063 (mp0) cc_final: 0.7825 (mt-10) REVERT: c 379 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7302 (ttp-110) REVERT: c 396 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7602 (tt0) outliers start: 32 outliers final: 19 residues processed: 179 average time/residue: 1.5506 time to fit residues: 294.7618 Evaluate side-chains 182 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 396 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 230 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 = 0.3591 r_free = 0.3591 target = 0.143579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125070 restraints weight = 11376.926| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.75 r_work: 0.3247 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10505 Z= 0.189 Angle : 0.532 7.014 14274 Z= 0.266 Chirality : 0.038 0.200 1833 Planarity : 0.003 0.044 1734 Dihedral : 6.192 59.049 2743 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.01 % Allowed : 9.57 % Favored : 87.42 % 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: 0.33 (0.27), residues: 1017 helix: 0.52 (0.28), residues: 342 sheet: 0.57 (0.43), residues: 138 loop : 0.05 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 210 HIS 0.005 0.001 HIS A 115 PHE 0.008 0.001 PHE b 399 TYR 0.009 0.001 TYR B 200 ARG 0.009 0.000 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8792 (p0) cc_final: 0.8546 (p0) REVERT: A 116 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7921 (mttt) REVERT: A 125 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8281 (tptp) REVERT: A 192 MET cc_start: 0.8549 (ptm) cc_final: 0.8144 (ppp) REVERT: B 134 MET cc_start: 0.9227 (tpp) cc_final: 0.8691 (tpt) REVERT: C 95 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8647 (tt) REVERT: C 114 ASN cc_start: 0.8265 (p0) cc_final: 0.7661 (t160) REVERT: C 256 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.6811 (mtp85) REVERT: a 270 GLU cc_start: 0.5952 (mm-30) cc_final: 0.3537 (tm-30) REVERT: a 282 ARG cc_start: 0.8514 (ttp-110) cc_final: 0.7930 (ttp-170) REVERT: b 379 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7878 (ttp-110) REVERT: c 303 GLU cc_start: 0.8037 (mp0) cc_final: 0.7790 (mt-10) REVERT: c 379 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7334 (ttp-110) REVERT: c 396 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7524 (tt0) outliers start: 28 outliers final: 16 residues processed: 180 average time/residue: 1.4589 time to fit residues: 279.5075 Evaluate side-chains 180 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 396 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.141399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122731 restraints weight = 11477.152| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.77 r_work: 0.3210 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10505 Z= 0.293 Angle : 0.598 7.347 14274 Z= 0.295 Chirality : 0.040 0.205 1833 Planarity : 0.004 0.045 1734 Dihedral : 6.399 57.090 2743 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.58 % Allowed : 10.32 % Favored : 87.10 % 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: 0.19 (0.26), residues: 1017 helix: 0.36 (0.28), residues: 342 sheet: 0.54 (0.44), residues: 138 loop : -0.02 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 386 HIS 0.006 0.001 HIS C 230 PHE 0.012 0.002 PHE b 399 TYR 0.019 0.002 TYR A 66 ARG 0.008 0.001 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8788 (p0) cc_final: 0.8524 (p0) REVERT: A 116 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7874 (mttt) REVERT: A 125 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8280 (tptp) REVERT: B 134 MET cc_start: 0.9249 (tpp) cc_final: 0.8789 (tpt) REVERT: C 114 ASN cc_start: 0.8280 (p0) cc_final: 0.7627 (t160) REVERT: C 256 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.6795 (mtp85) REVERT: a 270 GLU cc_start: 0.5887 (mm-30) cc_final: 0.3454 (tm-30) REVERT: a 282 ARG cc_start: 0.8505 (ttp-110) cc_final: 0.8022 (ttp-170) REVERT: c 303 GLU cc_start: 0.7971 (mp0) cc_final: 0.7725 (mt-10) REVERT: c 379 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7320 (ttp-110) outliers start: 24 outliers final: 17 residues processed: 171 average time/residue: 1.4660 time to fit residues: 267.0223 Evaluate side-chains 176 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123388 restraints weight = 11504.416| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.76 r_work: 0.3225 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10505 Z= 0.253 Angle : 0.566 7.243 14274 Z= 0.282 Chirality : 0.039 0.206 1833 Planarity : 0.003 0.045 1734 Dihedral : 6.196 55.944 2743 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.26 % Allowed : 10.65 % Favored : 87.10 % 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: 0.33 (0.27), residues: 1017 helix: 0.48 (0.28), residues: 336 sheet: 0.57 (0.44), residues: 138 loop : 0.08 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 283 HIS 0.005 0.001 HIS A 115 PHE 0.009 0.001 PHE b 399 TYR 0.018 0.001 TYR A 66 ARG 0.010 0.000 ARG b 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8770 (p0) cc_final: 0.8526 (p0) REVERT: A 116 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7891 (mttt) REVERT: A 125 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8291 (tptp) REVERT: A 192 MET cc_start: 0.8516 (ptm) cc_final: 0.8104 (ppp) REVERT: B 134 MET cc_start: 0.9242 (tpp) cc_final: 0.8782 (tpt) REVERT: C 256 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.6833 (mtp85) REVERT: a 270 GLU cc_start: 0.5969 (mm-30) cc_final: 0.3509 (tm-30) REVERT: a 282 ARG cc_start: 0.8512 (ttp-110) cc_final: 0.8033 (ttp-170) REVERT: a 332 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7230 (ttt) REVERT: a 401 ASP cc_start: 0.9026 (m-30) cc_final: 0.8811 (m-30) REVERT: c 303 GLU cc_start: 0.7971 (mp0) cc_final: 0.7709 (mt-10) REVERT: c 379 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7399 (ttp-110) outliers start: 21 outliers final: 16 residues processed: 166 average time/residue: 1.4589 time to fit residues: 257.8304 Evaluate side-chains 174 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 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 = 0.3585 r_free = 0.3585 target = 0.142948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124527 restraints weight = 11419.616| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.75 r_work: 0.3232 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10505 Z= 0.198 Angle : 0.534 6.964 14274 Z= 0.268 Chirality : 0.038 0.203 1833 Planarity : 0.003 0.045 1734 Dihedral : 5.929 53.464 2743 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.69 % Allowed : 10.32 % Favored : 86.99 % 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: 0.34 (0.27), residues: 1017 helix: 0.54 (0.28), residues: 342 sheet: 0.66 (0.44), residues: 138 loop : 0.01 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 283 HIS 0.004 0.001 HIS A 115 PHE 0.008 0.001 PHE b 399 TYR 0.015 0.001 TYR A 66 ARG 0.009 0.000 ARG b 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8736 (p0) cc_final: 0.8463 (p0) REVERT: A 116 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7858 (mttt) REVERT: A 125 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8268 (tptp) REVERT: B 134 MET cc_start: 0.9210 (tpp) cc_final: 0.8679 (tpt) REVERT: C 256 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.6759 (mtp85) REVERT: a 270 GLU cc_start: 0.5836 (mm-30) cc_final: 0.3386 (tm-30) REVERT: a 282 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.7988 (ttp-170) REVERT: a 332 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7184 (ttt) REVERT: b 379 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7310 (ttp80) REVERT: c 303 GLU cc_start: 0.7918 (mp0) cc_final: 0.7642 (mt-10) REVERT: c 379 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7344 (ttp-110) outliers start: 25 outliers final: 19 residues processed: 166 average time/residue: 1.5454 time to fit residues: 272.2057 Evaluate side-chains 174 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.122768 restraints weight = 11570.348| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.72 r_work: 0.3248 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10505 Z= 0.190 Angle : 0.537 8.066 14274 Z= 0.271 Chirality : 0.038 0.206 1833 Planarity : 0.003 0.044 1734 Dihedral : 5.796 51.864 2743 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.69 % Allowed : 10.65 % Favored : 86.67 % 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: 0.39 (0.27), residues: 1017 helix: 0.64 (0.28), residues: 339 sheet: 0.66 (0.44), residues: 138 loop : 0.01 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 210 HIS 0.004 0.001 HIS A 115 PHE 0.008 0.001 PHE b 399 TYR 0.015 0.001 TYR A 66 ARG 0.009 0.000 ARG b 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7405.32 seconds wall clock time: 133 minutes 40.81 seconds (8020.81 seconds total)