Starting phenix.real_space_refine on Sat Aug 23 07:49:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tyc_41713/08_2025/8tyc_41713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tyc_41713/08_2025/8tyc_41713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tyc_41713/08_2025/8tyc_41713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tyc_41713/08_2025/8tyc_41713.map" model { file = "/net/cci-nas-00/data/ceres_data/8tyc_41713/08_2025/8tyc_41713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tyc_41713/08_2025/8tyc_41713.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.045 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 93 5.16 5 C 6603 2.51 5 N 1712 2.21 5 O 2220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10628 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1536 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1583 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 195} Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1548 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "a" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1256 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain breaks: 1 Chain: "b" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1269 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "c" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1306 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} 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: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" 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: "Y" 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: "Z" 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: "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: 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: "f" 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: "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: "h" 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: "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: "C" 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: "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 Time building chain proxies: 2.89, per 1000 atoms: 0.27 Number of scatterers: 10628 At special positions: 0 Unit cell: (111.622, 109.956, 109.123, 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 93 16.00 O 2220 8.00 N 1712 7.00 C 6603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.02 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.01 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.04 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=2.01 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 Z 4 " - " MAN Z 5 " " MAN f 4 " - " MAN f 5 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA Z 3 " - " MAN Z 4 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 6 " " BMA f 3 " - " MAN f 6 " " BMA h 3 " - " MAN h 6 " BETA1-3 " NAG Q 1 " - " FUC Q 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " BETA1-6 " NAG W 1 " - " FUC W 3 " NAG-ASN " NAG C 301 " - " ASN C 99 " " NAG D 1 " - " ASN A 119 " " NAG E 1 " - " ASN A 79 " " NAG F 1 " - " ASN A 89 " " NAG G 1 " - " ASN A 99 " " NAG I 1 " - " ASN A 109 " " NAG J 1 " - " ASN A 167 " " NAG K 1 " - " ASN A 224 " " NAG M 1 " - " ASN B 99 " " NAG N 1 " - " ASN B 224 " " NAG O 1 " - " ASN B 167 " " NAG P 1 " - " ASN B 119 " " NAG Q 1 " - " ASN B 109 " " NAG R 1 " - " ASN B 89 " " NAG S 1 " - " ASN B 79 " " NAG T 1 " - " ASN C 119 " " NAG U 1 " - " ASN C 79 " " NAG V 1 " - " ASN C 89 " " NAG W 1 " - " ASN C 109 " " NAG X 1 " - " ASN C 167 " " NAG Y 1 " - " ASN C 224 " " NAG Z 1 " - " ASN a 365 " " NAG a 701 " - " ASN a 395 " " NAG a 702 " - " ASN a 390 " " NAG b 701 " - " ASN b 390 " " NAG c 701 " - " ASN c 395 " " NAG c 702 " - " ASN c 390 " " NAG d 1 " - " ASN a 373 " " NAG e 1 " - " ASN b 373 " " NAG f 1 " - " ASN b 365 " " NAG g 1 " - " ASN b 395 " " NAG h 1 " - " ASN c 365 " " NAG i 1 " - " ASN c 373 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 330.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 15 sheets defined 43.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.637A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.946A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 142 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 Processing helix chain 'B' and resid 183 through 195 removed outlier: 4.124A pdb=" N GLN B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.194A pdb=" N MET C 80 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 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 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.637A pdb=" N ARG C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.948A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.562A pdb=" N UNK H 32 " --> pdb=" O UNK H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.528A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU a 344 " --> pdb=" O ALA a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 420 Processing helix chain 'b' and resid 281 through 285 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 Processing helix chain 'b' and resid 334 through 345 removed outlier: 4.968A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 347 through 359 Processing helix chain 'b' and resid 399 through 420 Processing helix chain 'c' and resid 281 through 285 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: 3.559A pdb=" N GLN c 324 " --> pdb=" O LYS c 320 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.599A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.500A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 396 through 398 No H-bonds generated for 'chain 'c' and resid 396 through 398' Processing helix chain 'c' and resid 399 through 420 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 87 removed outlier: 3.600A pdb=" N GLY A 102 " --> pdb=" O THR A 225 " (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 84 through 87 Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.541A pdb=" N GLY C 102 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.012A pdb=" N UNK H 45 " --> pdb=" O UNK H 39 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N UNK H 39 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N UNK H 47 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N UNK H 37 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N UNK H 49 " --> pdb=" O UNK H 35 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N UNK H 35 " --> pdb=" O UNK H 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 52 through 53 removed outlier: 4.346A pdb=" N UNK L 44 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N UNK L 37 " --> pdb=" O UNK L 44 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N UNK L 46 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N UNK L 35 " --> pdb=" O UNK L 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB5, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB6, first strand: chain 'c' and resid 388 through 389 425 hydrogen bonds defined for protein. 1065 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: 1.57 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2494 1.33 - 1.47: 3481 1.47 - 1.61: 4690 1.61 - 1.75: 8 1.75 - 1.89: 139 Bond restraints: 10812 Sorted by residual: bond pdb=" CA SER C 121 " pdb=" CB SER C 121 " ideal model delta sigma weight residual 1.527 1.427 0.100 1.15e-02 7.56e+03 7.55e+01 bond pdb=" CB LEU B 259 " pdb=" CG LEU B 259 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" CB HIS A 115 " pdb=" CG HIS A 115 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.66e+01 bond pdb=" NE1 TRP b 386 " pdb=" CE2 TRP b 386 " ideal model delta sigma weight residual 1.370 1.309 0.061 1.10e-02 8.26e+03 3.10e+01 bond pdb=" CB LEU A 259 " pdb=" CG LEU A 259 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.96e+01 ... (remaining 10807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 13517 3.09 - 6.18: 1087 6.18 - 9.27: 68 9.27 - 12.36: 5 12.36 - 15.44: 2 Bond angle restraints: 14679 Sorted by residual: angle pdb=" N ILE b 350 " pdb=" CA ILE b 350 " pdb=" C ILE b 350 " ideal model delta sigma weight residual 111.58 101.80 9.78 1.06e+00 8.90e-01 8.51e+01 angle pdb=" N SER c 269 " pdb=" CA SER c 269 " pdb=" C SER c 269 " ideal model delta sigma weight residual 111.07 119.14 -8.07 1.07e+00 8.73e-01 5.69e+01 angle pdb=" C ALA c 328 " pdb=" N PRO c 329 " pdb=" CA PRO c 329 " ideal model delta sigma weight residual 120.31 127.42 -7.11 9.80e-01 1.04e+00 5.26e+01 angle pdb=" N LEU c 349 " pdb=" CA LEU c 349 " pdb=" C LEU c 349 " ideal model delta sigma weight residual 111.69 103.48 8.21 1.23e+00 6.61e-01 4.45e+01 angle pdb=" CA ASP a 357 " pdb=" CB ASP a 357 " pdb=" CG ASP a 357 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.37e+01 ... (remaining 14674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 7118 21.41 - 42.83: 207 42.83 - 64.24: 48 64.24 - 85.66: 72 85.66 - 107.07: 42 Dihedral angle restraints: 7487 sinusoidal: 3742 harmonic: 3745 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 -141.13 55.13 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" CA CYS B 118 " pdb=" CB CYS B 118 " pdb=" SG CYS B 118 " pdb=" SG CYS B 155 " ideal model delta sinusoidal sigma weight residual 79.00 7.75 71.25 1 2.00e+01 2.50e-03 1.63e+01 dihedral pdb=" O4 BMA h 3 " pdb=" C4 BMA h 3 " pdb=" C5 BMA h 3 " pdb=" O5 BMA h 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.36 107.07 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 7484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1531 0.183 - 0.366: 289 0.366 - 0.549: 81 0.549 - 0.732: 1 0.732 - 0.915: 1 Chirality restraints: 1903 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.14e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.77e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.75e+02 ... (remaining 1900 not shown) Planarity restraints: 1795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.11e+03 pdb=" C7 NAG T 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.127 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 1 " -0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG g 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG g 1 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG g 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG g 1 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 2 " -0.312 2.00e-02 2.50e+03 2.63e-01 8.66e+02 pdb=" C7 NAG g 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG g 2 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG g 2 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG g 2 " -0.037 2.00e-02 2.50e+03 ... (remaining 1792 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3855 2.87 - 3.38: 10103 3.38 - 3.89: 17579 3.89 - 4.39: 21043 4.39 - 4.90: 32250 Nonbonded interactions: 84830 Sorted by model distance: nonbonded pdb=" O ALA A 195 " pdb=" O GLY A 197 " model vdw 2.365 3.040 nonbonded pdb=" N ASP C 122 " pdb=" N ALA C 123 " model vdw 2.367 2.560 nonbonded pdb=" OD2 ASP B 251 " pdb=" NZ LYS c 339 " model vdw 2.369 3.120 nonbonded pdb=" O SER C 121 " pdb=" OG SER C 121 " model vdw 2.376 3.040 nonbonded pdb=" N ASP B 251 " pdb=" OD1 ASP B 251 " model vdw 2.388 3.120 ... (remaining 84825 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 60 through 171 or resid 179 through 259)) selection = (chain 'C' and (resid 60 through 171 or resid 179 through 259)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) } ncs_group { reference = (chain 'H' and resid 4 through 111) selection = chain 'L' } ncs_group { reference = chain 'Z' selection = chain 'f' selection = chain 'h' } ncs_group { reference = (chain 'a' and resid 260 through 701) selection = (chain 'b' and (resid 260 through 268 or resid 276 through 701)) selection = (chain 'c' and (resid 260 through 268 or resid 276 through 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.240 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.133 10912 Z= 1.161 Angle : 1.834 15.444 14959 Z= 1.076 Chirality : 0.154 0.915 1903 Planarity : 0.016 0.297 1762 Dihedral : 16.239 107.073 4999 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.25), residues: 1038 helix: -0.37 (0.25), residues: 365 sheet: 1.14 (0.48), residues: 111 loop : 0.79 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 250 TYR 0.063 0.009 TYR C 253 PHE 0.025 0.004 PHE A 233 TRP 0.052 0.010 TRP C 196 HIS 0.012 0.003 HIS a 354 Details of bonding type rmsd covalent geometry : bond 0.02115 (10812) covalent geometry : angle 1.75336 (14679) SS BOND : bond 0.01104 ( 20) SS BOND : angle 3.01158 ( 40) hydrogen bonds : bond 0.18766 ( 425) hydrogen bonds : angle 7.37351 ( 1065) link_ALPHA1-2 : bond 0.08386 ( 3) link_ALPHA1-2 : angle 5.00615 ( 9) link_ALPHA1-3 : bond 0.08120 ( 3) link_ALPHA1-3 : angle 4.58051 ( 9) link_ALPHA1-6 : bond 0.05101 ( 3) link_ALPHA1-6 : angle 2.88869 ( 9) link_BETA1-3 : bond 0.10280 ( 1) link_BETA1-3 : angle 6.14907 ( 3) link_BETA1-4 : bond 0.07150 ( 36) link_BETA1-4 : angle 5.51331 ( 108) link_BETA1-6 : bond 0.04972 ( 1) link_BETA1-6 : angle 2.70987 ( 3) link_NAG-ASN : bond 0.07425 ( 33) link_NAG-ASN : angle 3.03249 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 405 GLN cc_start: 0.8519 (tp40) cc_final: 0.7977 (tp-100) REVERT: a 409 ASN cc_start: 0.8895 (m-40) cc_final: 0.8621 (m-40) REVERT: c 406 GLN cc_start: 0.8649 (tp40) cc_final: 0.8214 (tp-100) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1283 time to fit residues: 54.9539 Evaluate side-chains 179 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 92 HIS B 165 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN b 348 GLN b 409 ASN c 348 GLN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.111867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.087909 restraints weight = 27049.216| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 4.20 r_work: 0.3343 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10912 Z= 0.183 Angle : 0.950 19.632 14959 Z= 0.441 Chirality : 0.050 0.619 1903 Planarity : 0.004 0.041 1762 Dihedral : 12.988 83.811 2987 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.94 % Allowed : 9.88 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.25), residues: 1038 helix: 0.89 (0.27), residues: 351 sheet: 2.32 (0.50), residues: 93 loop : 0.45 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 379 TYR 0.018 0.002 TYR A 94 PHE 0.018 0.002 PHE a 399 TRP 0.030 0.002 TRP C 210 HIS 0.006 0.002 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00374 (10812) covalent geometry : angle 0.84590 (14679) SS BOND : bond 0.00813 ( 20) SS BOND : angle 2.69005 ( 40) hydrogen bonds : bond 0.05359 ( 425) hydrogen bonds : angle 5.71849 ( 1065) link_ALPHA1-2 : bond 0.00701 ( 3) link_ALPHA1-2 : angle 2.24179 ( 9) link_ALPHA1-3 : bond 0.01624 ( 3) link_ALPHA1-3 : angle 1.40411 ( 9) link_ALPHA1-6 : bond 0.00884 ( 3) link_ALPHA1-6 : angle 1.86755 ( 9) link_BETA1-3 : bond 0.01178 ( 1) link_BETA1-3 : angle 2.06718 ( 3) link_BETA1-4 : bond 0.01390 ( 36) link_BETA1-4 : angle 3.89086 ( 108) link_BETA1-6 : bond 0.00348 ( 1) link_BETA1-6 : angle 1.54401 ( 3) link_NAG-ASN : bond 0.00745 ( 33) link_NAG-ASN : angle 3.12827 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.7406 (m-80) cc_final: 0.7181 (m-10) REVERT: B 80 MET cc_start: 0.7903 (mmt) cc_final: 0.7626 (mmp) REVERT: B 214 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7834 (mtm) REVERT: C 85 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8182 (p) REVERT: C 251 ASP cc_start: 0.8712 (m-30) cc_final: 0.8239 (m-30) REVERT: a 282 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7293 (tmm-80) REVERT: a 304 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8738 (mtpp) REVERT: a 405 GLN cc_start: 0.8794 (tp40) cc_final: 0.7612 (tp-100) REVERT: a 409 ASN cc_start: 0.9102 (m-40) cc_final: 0.8846 (m-40) REVERT: a 410 MET cc_start: 0.7852 (mmm) cc_final: 0.7585 (mmm) REVERT: b 287 GLU cc_start: 0.9154 (pt0) cc_final: 0.8769 (pp20) REVERT: b 295 ASN cc_start: 0.8290 (p0) cc_final: 0.7937 (t0) REVERT: b 401 ASP cc_start: 0.9175 (t70) cc_final: 0.8866 (t70) REVERT: b 405 GLN cc_start: 0.9148 (mt0) cc_final: 0.8900 (mp10) REVERT: c 289 GLU cc_start: 0.8079 (mp0) cc_final: 0.7751 (pm20) REVERT: c 304 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8588 (mtmm) REVERT: c 371 TYR cc_start: 0.8477 (p90) cc_final: 0.8084 (p90) REVERT: c 406 GLN cc_start: 0.8645 (tp40) cc_final: 0.8129 (tp-100) REVERT: c 410 MET cc_start: 0.7487 (mmm) cc_final: 0.6982 (mmm) outliers start: 28 outliers final: 10 residues processed: 231 average time/residue: 0.1124 time to fit residues: 36.2246 Evaluate side-chains 193 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 282 ARG Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN C 179 HIS c 342 ASN c 374 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.085186 restraints weight = 27448.884| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.21 r_work: 0.3299 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10912 Z= 0.182 Angle : 0.885 18.709 14959 Z= 0.411 Chirality : 0.049 0.556 1903 Planarity : 0.003 0.043 1762 Dihedral : 10.140 78.537 2987 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.84 % Allowed : 12.30 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.25), residues: 1038 helix: 1.01 (0.28), residues: 362 sheet: 1.85 (0.50), residues: 106 loop : 0.14 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 379 TYR 0.017 0.002 TYR c 366 PHE 0.014 0.001 PHE a 399 TRP 0.021 0.001 TRP C 210 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00391 (10812) covalent geometry : angle 0.78056 (14679) SS BOND : bond 0.01023 ( 20) SS BOND : angle 3.77604 ( 40) hydrogen bonds : bond 0.04666 ( 425) hydrogen bonds : angle 5.25410 ( 1065) link_ALPHA1-2 : bond 0.00435 ( 3) link_ALPHA1-2 : angle 2.00564 ( 9) link_ALPHA1-3 : bond 0.01377 ( 3) link_ALPHA1-3 : angle 0.85527 ( 9) link_ALPHA1-6 : bond 0.00815 ( 3) link_ALPHA1-6 : angle 1.78182 ( 9) link_BETA1-3 : bond 0.01288 ( 1) link_BETA1-3 : angle 2.80858 ( 3) link_BETA1-4 : bond 0.01185 ( 36) link_BETA1-4 : angle 3.23185 ( 108) link_BETA1-6 : bond 0.00230 ( 1) link_BETA1-6 : angle 1.83032 ( 3) link_NAG-ASN : bond 0.00706 ( 33) link_NAG-ASN : angle 3.13804 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7811 (mp0) REVERT: A 211 ASP cc_start: 0.8046 (m-30) cc_final: 0.7601 (p0) REVERT: A 259 LEU cc_start: 0.7865 (tp) cc_final: 0.7587 (tt) REVERT: C 251 ASP cc_start: 0.8771 (m-30) cc_final: 0.8303 (m-30) REVERT: a 308 GLU cc_start: 0.8217 (mp0) cc_final: 0.7493 (mt-10) REVERT: a 409 ASN cc_start: 0.9333 (m-40) cc_final: 0.9100 (m-40) REVERT: a 410 MET cc_start: 0.7859 (mmm) cc_final: 0.7631 (mmm) REVERT: b 283 TRP cc_start: 0.7717 (m100) cc_final: 0.7445 (m100) REVERT: b 287 GLU cc_start: 0.9159 (pt0) cc_final: 0.8801 (pp20) REVERT: b 289 GLU cc_start: 0.7659 (mp0) cc_final: 0.7266 (mp0) REVERT: b 304 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8577 (mtpp) REVERT: b 327 LYS cc_start: 0.7966 (ptmt) cc_final: 0.7347 (pttt) REVERT: b 352 LYS cc_start: 0.8458 (tttm) cc_final: 0.8158 (tttt) REVERT: b 401 ASP cc_start: 0.9133 (t70) cc_final: 0.8813 (t70) REVERT: c 284 MET cc_start: 0.8449 (mtt) cc_final: 0.8164 (mtp) REVERT: c 304 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8488 (mtpp) REVERT: c 308 GLU cc_start: 0.8192 (mp0) cc_final: 0.7857 (mp0) REVERT: c 371 TYR cc_start: 0.8612 (p90) cc_final: 0.8091 (p90) REVERT: c 406 GLN cc_start: 0.8685 (tp40) cc_final: 0.8373 (tp-100) outliers start: 27 outliers final: 12 residues processed: 205 average time/residue: 0.1064 time to fit residues: 30.9439 Evaluate side-chains 191 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS b 405 GLN c 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.085217 restraints weight = 27531.963| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.21 r_work: 0.3301 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10912 Z= 0.150 Angle : 0.824 18.920 14959 Z= 0.386 Chirality : 0.047 0.504 1903 Planarity : 0.003 0.044 1762 Dihedral : 8.425 69.965 2987 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.52 % Allowed : 13.67 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.26), residues: 1038 helix: 1.10 (0.28), residues: 362 sheet: 1.36 (0.45), residues: 127 loop : 0.00 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 379 TYR 0.025 0.001 TYR c 366 PHE 0.011 0.001 PHE a 399 TRP 0.021 0.001 TRP C 210 HIS 0.005 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00311 (10812) covalent geometry : angle 0.72810 (14679) SS BOND : bond 0.00887 ( 20) SS BOND : angle 3.87667 ( 40) hydrogen bonds : bond 0.04092 ( 425) hydrogen bonds : angle 4.99865 ( 1065) link_ALPHA1-2 : bond 0.00358 ( 3) link_ALPHA1-2 : angle 1.90579 ( 9) link_ALPHA1-3 : bond 0.01311 ( 3) link_ALPHA1-3 : angle 0.95873 ( 9) link_ALPHA1-6 : bond 0.00910 ( 3) link_ALPHA1-6 : angle 1.80861 ( 9) link_BETA1-3 : bond 0.01119 ( 1) link_BETA1-3 : angle 2.74439 ( 3) link_BETA1-4 : bond 0.01114 ( 36) link_BETA1-4 : angle 2.93581 ( 108) link_BETA1-6 : bond 0.00184 ( 1) link_BETA1-6 : angle 1.62993 ( 3) link_NAG-ASN : bond 0.00587 ( 33) link_NAG-ASN : angle 2.73423 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7999 (tp30) cc_final: 0.7743 (tp30) REVERT: A 76 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7773 (mp0) REVERT: A 211 ASP cc_start: 0.7951 (m-30) cc_final: 0.7670 (p0) REVERT: A 259 LEU cc_start: 0.7856 (tp) cc_final: 0.7565 (tt) REVERT: C 251 ASP cc_start: 0.8793 (m-30) cc_final: 0.8352 (m-30) REVERT: a 304 LYS cc_start: 0.9383 (mtpp) cc_final: 0.9172 (mtpp) REVERT: a 308 GLU cc_start: 0.8234 (mp0) cc_final: 0.7539 (mt-10) REVERT: a 396 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7216 (tm-30) REVERT: a 406 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8849 (tp40) REVERT: b 283 TRP cc_start: 0.7654 (m100) cc_final: 0.7371 (m100) REVERT: b 287 GLU cc_start: 0.9153 (pt0) cc_final: 0.8767 (pp20) REVERT: b 289 GLU cc_start: 0.7626 (mp0) cc_final: 0.7202 (mp0) REVERT: b 304 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8600 (mtpp) REVERT: b 306 ASP cc_start: 0.8911 (p0) cc_final: 0.8672 (p0) REVERT: b 327 LYS cc_start: 0.7920 (ptmt) cc_final: 0.7438 (pttt) REVERT: b 352 LYS cc_start: 0.8495 (tttm) cc_final: 0.8195 (tttt) REVERT: c 308 GLU cc_start: 0.8207 (mp0) cc_final: 0.7915 (mp0) REVERT: c 371 TYR cc_start: 0.8613 (p90) cc_final: 0.8213 (p90) REVERT: c 405 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8590 (tm-30) REVERT: c 406 GLN cc_start: 0.8722 (tp40) cc_final: 0.8442 (tp40) REVERT: c 410 MET cc_start: 0.7389 (mmm) cc_final: 0.7044 (mmm) outliers start: 24 outliers final: 11 residues processed: 212 average time/residue: 0.0985 time to fit residues: 30.2979 Evaluate side-chains 194 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 405 GLN b 305 HIS ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.106439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.082491 restraints weight = 27987.119| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.16 r_work: 0.3273 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10912 Z= 0.211 Angle : 0.890 23.059 14959 Z= 0.416 Chirality : 0.049 0.537 1903 Planarity : 0.004 0.044 1762 Dihedral : 8.125 63.722 2987 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.58 % Allowed : 13.46 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.26), residues: 1038 helix: 1.14 (0.28), residues: 356 sheet: 1.25 (0.43), residues: 133 loop : -0.13 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 250 TYR 0.031 0.002 TYR c 366 PHE 0.010 0.002 PHE a 316 TRP 0.022 0.002 TRP C 210 HIS 0.008 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00471 (10812) covalent geometry : angle 0.80060 (14679) SS BOND : bond 0.00939 ( 20) SS BOND : angle 4.19219 ( 40) hydrogen bonds : bond 0.04462 ( 425) hydrogen bonds : angle 5.00009 ( 1065) link_ALPHA1-2 : bond 0.00231 ( 3) link_ALPHA1-2 : angle 2.12008 ( 9) link_ALPHA1-3 : bond 0.01224 ( 3) link_ALPHA1-3 : angle 1.14943 ( 9) link_ALPHA1-6 : bond 0.00873 ( 3) link_ALPHA1-6 : angle 1.73979 ( 9) link_BETA1-3 : bond 0.01123 ( 1) link_BETA1-3 : angle 2.75317 ( 3) link_BETA1-4 : bond 0.00961 ( 36) link_BETA1-4 : angle 2.82684 ( 108) link_BETA1-6 : bond 0.00147 ( 1) link_BETA1-6 : angle 2.20444 ( 3) link_NAG-ASN : bond 0.00613 ( 33) link_NAG-ASN : angle 2.78077 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8147 (tp30) cc_final: 0.7878 (tp30) REVERT: A 76 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7787 (mp0) REVERT: A 259 LEU cc_start: 0.7830 (tp) cc_final: 0.7546 (tt) REVERT: B 130 ASP cc_start: 0.8433 (t0) cc_final: 0.8155 (t0) REVERT: C 251 ASP cc_start: 0.8851 (m-30) cc_final: 0.8512 (m-30) REVERT: a 308 GLU cc_start: 0.8284 (mp0) cc_final: 0.7706 (mt-10) REVERT: a 371 TYR cc_start: 0.8370 (p90) cc_final: 0.8132 (p90) REVERT: a 396 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7355 (tm-30) REVERT: a 406 GLN cc_start: 0.9135 (tp-100) cc_final: 0.8914 (tp40) REVERT: b 283 TRP cc_start: 0.7671 (m100) cc_final: 0.7377 (m100) REVERT: b 287 GLU cc_start: 0.9228 (pt0) cc_final: 0.8844 (pp20) REVERT: b 289 GLU cc_start: 0.7880 (mp0) cc_final: 0.7408 (mp0) REVERT: b 295 ASN cc_start: 0.8451 (p0) cc_final: 0.8250 (p0) REVERT: b 304 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8732 (mtpp) REVERT: b 327 LYS cc_start: 0.7872 (ptmt) cc_final: 0.7344 (pttt) REVERT: c 304 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8674 (mtmm) REVERT: c 308 GLU cc_start: 0.8286 (mp0) cc_final: 0.7575 (mt-10) REVERT: c 406 GLN cc_start: 0.8731 (tp40) cc_final: 0.8205 (tp-100) REVERT: c 410 MET cc_start: 0.7582 (mmm) cc_final: 0.7019 (mmm) outliers start: 34 outliers final: 21 residues processed: 217 average time/residue: 0.1010 time to fit residues: 31.5878 Evaluate side-chains 202 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 367 SER Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 392 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 81 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 106 optimal weight: 0.0870 chunk 93 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 405 GLN b 405 GLN b 406 GLN c 302 ASN ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 374 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.107607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.083919 restraints weight = 27805.907| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 4.14 r_work: 0.3298 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10912 Z= 0.149 Angle : 0.834 19.605 14959 Z= 0.388 Chirality : 0.047 0.507 1903 Planarity : 0.003 0.045 1762 Dihedral : 7.668 58.682 2987 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.73 % Allowed : 14.83 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.26), residues: 1038 helix: 1.23 (0.29), residues: 357 sheet: 1.46 (0.48), residues: 105 loop : -0.12 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG c 356 TYR 0.024 0.001 TYR c 366 PHE 0.012 0.001 PHE c 399 TRP 0.023 0.001 TRP C 210 HIS 0.005 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00315 (10812) covalent geometry : angle 0.74291 (14679) SS BOND : bond 0.00777 ( 20) SS BOND : angle 4.12287 ( 40) hydrogen bonds : bond 0.03895 ( 425) hydrogen bonds : angle 4.86863 ( 1065) link_ALPHA1-2 : bond 0.00241 ( 3) link_ALPHA1-2 : angle 2.04513 ( 9) link_ALPHA1-3 : bond 0.01254 ( 3) link_ALPHA1-3 : angle 1.07904 ( 9) link_ALPHA1-6 : bond 0.00979 ( 3) link_ALPHA1-6 : angle 1.69249 ( 9) link_BETA1-3 : bond 0.01208 ( 1) link_BETA1-3 : angle 2.77948 ( 3) link_BETA1-4 : bond 0.00980 ( 36) link_BETA1-4 : angle 2.66425 ( 108) link_BETA1-6 : bond 0.00175 ( 1) link_BETA1-6 : angle 1.69187 ( 3) link_NAG-ASN : bond 0.00637 ( 33) link_NAG-ASN : angle 2.75082 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8098 (tp30) cc_final: 0.7806 (tm-30) REVERT: A 76 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7743 (mp0) REVERT: A 211 ASP cc_start: 0.8000 (m-30) cc_final: 0.7450 (p0) REVERT: A 259 LEU cc_start: 0.7816 (tp) cc_final: 0.7351 (tt) REVERT: B 130 ASP cc_start: 0.8455 (t0) cc_final: 0.8156 (t0) REVERT: B 214 MET cc_start: 0.8615 (mtm) cc_final: 0.8312 (ttt) REVERT: C 82 MET cc_start: 0.8065 (ptp) cc_final: 0.7656 (pmm) REVERT: C 233 PHE cc_start: 0.8426 (t80) cc_final: 0.8116 (t80) REVERT: C 251 ASP cc_start: 0.8805 (m-30) cc_final: 0.8490 (m-30) REVERT: a 308 GLU cc_start: 0.8228 (mp0) cc_final: 0.7754 (mt-10) REVERT: a 396 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7348 (tm-30) REVERT: a 406 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8858 (tp40) REVERT: b 283 TRP cc_start: 0.7544 (m100) cc_final: 0.7252 (m100) REVERT: b 287 GLU cc_start: 0.9226 (pt0) cc_final: 0.8850 (pp20) REVERT: b 289 GLU cc_start: 0.7808 (mp0) cc_final: 0.7280 (mp0) REVERT: b 295 ASN cc_start: 0.8427 (p0) cc_final: 0.8192 (p0) REVERT: b 311 ASP cc_start: 0.9152 (m-30) cc_final: 0.8666 (t0) REVERT: b 312 MET cc_start: 0.9008 (mmp) cc_final: 0.8771 (mmp) REVERT: b 327 LYS cc_start: 0.7865 (ptmt) cc_final: 0.7292 (pttt) REVERT: b 332 MET cc_start: 0.7505 (mmm) cc_final: 0.7035 (tpt) REVERT: b 406 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8450 (mm-40) REVERT: b 413 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8385 (tm-30) REVERT: c 304 LYS cc_start: 0.8865 (mtpp) cc_final: 0.8580 (mtmm) REVERT: c 308 GLU cc_start: 0.8252 (mp0) cc_final: 0.7444 (mt-10) REVERT: c 406 GLN cc_start: 0.8734 (tp40) cc_final: 0.8451 (tp40) REVERT: c 410 MET cc_start: 0.7555 (mmm) cc_final: 0.7133 (mmm) outliers start: 26 outliers final: 18 residues processed: 212 average time/residue: 0.1010 time to fit residues: 30.7716 Evaluate side-chains 200 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 406 GLN Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 120 optimal weight: 0.0980 chunk 4 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** C 74 ASN a 405 GLN c 305 HIS c 374 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.108179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.084681 restraints weight = 27670.648| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.11 r_work: 0.3315 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10912 Z= 0.133 Angle : 0.825 18.217 14959 Z= 0.387 Chirality : 0.047 0.494 1903 Planarity : 0.003 0.046 1762 Dihedral : 7.271 57.460 2987 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.52 % Allowed : 15.77 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.26), residues: 1038 helix: 1.28 (0.29), residues: 355 sheet: 1.50 (0.45), residues: 127 loop : -0.13 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 250 TYR 0.019 0.001 TYR c 366 PHE 0.012 0.001 PHE a 399 TRP 0.022 0.001 TRP C 210 HIS 0.006 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00271 (10812) covalent geometry : angle 0.73804 (14679) SS BOND : bond 0.00886 ( 20) SS BOND : angle 4.22311 ( 40) hydrogen bonds : bond 0.03778 ( 425) hydrogen bonds : angle 4.81777 ( 1065) link_ALPHA1-2 : bond 0.00164 ( 3) link_ALPHA1-2 : angle 2.00716 ( 9) link_ALPHA1-3 : bond 0.01299 ( 3) link_ALPHA1-3 : angle 1.03755 ( 9) link_ALPHA1-6 : bond 0.01058 ( 3) link_ALPHA1-6 : angle 1.68988 ( 9) link_BETA1-3 : bond 0.01182 ( 1) link_BETA1-3 : angle 2.74768 ( 3) link_BETA1-4 : bond 0.00986 ( 36) link_BETA1-4 : angle 2.59314 ( 108) link_BETA1-6 : bond 0.00262 ( 1) link_BETA1-6 : angle 1.60969 ( 3) link_NAG-ASN : bond 0.00526 ( 33) link_NAG-ASN : angle 2.54802 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7717 (mp0) REVERT: A 259 LEU cc_start: 0.7831 (tp) cc_final: 0.7387 (tt) REVERT: B 130 ASP cc_start: 0.8439 (t0) cc_final: 0.8122 (t0) REVERT: B 214 MET cc_start: 0.8619 (mtm) cc_final: 0.8322 (ttt) REVERT: C 82 MET cc_start: 0.8036 (ptp) cc_final: 0.7681 (pmm) REVERT: C 233 PHE cc_start: 0.8446 (t80) cc_final: 0.8113 (t80) REVERT: C 251 ASP cc_start: 0.8822 (m-30) cc_final: 0.8548 (m-30) REVERT: a 308 GLU cc_start: 0.8176 (mp0) cc_final: 0.7679 (mt-10) REVERT: a 396 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7276 (tm-30) REVERT: a 406 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8830 (tp40) REVERT: b 283 TRP cc_start: 0.7474 (m100) cc_final: 0.7171 (m100) REVERT: b 287 GLU cc_start: 0.9236 (pt0) cc_final: 0.8869 (pp20) REVERT: b 289 GLU cc_start: 0.7691 (mp0) cc_final: 0.7194 (mp0) REVERT: b 295 ASN cc_start: 0.8421 (p0) cc_final: 0.8200 (p0) REVERT: b 311 ASP cc_start: 0.9134 (m-30) cc_final: 0.8653 (t0) REVERT: b 312 MET cc_start: 0.9087 (mmp) cc_final: 0.8779 (mmp) REVERT: b 332 MET cc_start: 0.7530 (mmm) cc_final: 0.7080 (tpt) REVERT: b 339 LYS cc_start: 0.8377 (mptt) cc_final: 0.8150 (mmtm) REVERT: b 413 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8413 (tm-30) REVERT: c 306 ASP cc_start: 0.8334 (p0) cc_final: 0.8133 (p0) REVERT: c 308 GLU cc_start: 0.8154 (mp0) cc_final: 0.7373 (mt-10) outliers start: 24 outliers final: 19 residues processed: 210 average time/residue: 0.1022 time to fit residues: 30.7340 Evaluate side-chains 201 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 104 optimal weight: 0.0370 chunk 85 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- 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 406 GLN c 374 HIS c 406 GLN ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.108468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.085232 restraints weight = 27394.874| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 4.06 r_work: 0.3327 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10912 Z= 0.131 Angle : 0.830 18.645 14959 Z= 0.389 Chirality : 0.046 0.487 1903 Planarity : 0.003 0.046 1762 Dihedral : 6.978 56.748 2987 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.52 % Allowed : 16.51 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1038 helix: 1.31 (0.29), residues: 355 sheet: 1.42 (0.44), residues: 137 loop : -0.11 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 282 TYR 0.019 0.001 TYR c 366 PHE 0.012 0.001 PHE a 262 TRP 0.025 0.001 TRP C 210 HIS 0.005 0.001 HIS c 305 Details of bonding type rmsd covalent geometry : bond 0.00273 (10812) covalent geometry : angle 0.74555 (14679) SS BOND : bond 0.00893 ( 20) SS BOND : angle 4.28890 ( 40) hydrogen bonds : bond 0.03690 ( 425) hydrogen bonds : angle 4.73036 ( 1065) link_ALPHA1-2 : bond 0.00135 ( 3) link_ALPHA1-2 : angle 1.99660 ( 9) link_ALPHA1-3 : bond 0.01270 ( 3) link_ALPHA1-3 : angle 1.02028 ( 9) link_ALPHA1-6 : bond 0.01089 ( 3) link_ALPHA1-6 : angle 1.62709 ( 9) link_BETA1-3 : bond 0.01178 ( 1) link_BETA1-3 : angle 2.71877 ( 3) link_BETA1-4 : bond 0.00983 ( 36) link_BETA1-4 : angle 2.54885 ( 108) link_BETA1-6 : bond 0.00266 ( 1) link_BETA1-6 : angle 1.57613 ( 3) link_NAG-ASN : bond 0.00521 ( 33) link_NAG-ASN : angle 2.47958 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7699 (mp0) REVERT: A 251 ASP cc_start: 0.7995 (m-30) cc_final: 0.7707 (t0) REVERT: A 259 LEU cc_start: 0.7861 (tp) cc_final: 0.7440 (tt) REVERT: B 130 ASP cc_start: 0.8442 (t0) cc_final: 0.8115 (t0) REVERT: B 214 MET cc_start: 0.8584 (mtm) cc_final: 0.8285 (ttt) REVERT: C 233 PHE cc_start: 0.8399 (t80) cc_final: 0.8069 (t80) REVERT: C 251 ASP cc_start: 0.8797 (m-30) cc_final: 0.8534 (m-30) REVERT: a 308 GLU cc_start: 0.8132 (mp0) cc_final: 0.7672 (mt-10) REVERT: a 396 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7215 (tm-30) REVERT: b 283 TRP cc_start: 0.7346 (m100) cc_final: 0.7029 (m100) REVERT: b 289 GLU cc_start: 0.7649 (mp0) cc_final: 0.7148 (mp0) REVERT: b 295 ASN cc_start: 0.8442 (p0) cc_final: 0.8224 (p0) REVERT: b 311 ASP cc_start: 0.9126 (m-30) cc_final: 0.8850 (m-30) REVERT: b 332 MET cc_start: 0.7584 (mmm) cc_final: 0.7146 (tpt) REVERT: b 413 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8401 (tm-30) REVERT: c 308 GLU cc_start: 0.8132 (mp0) cc_final: 0.7858 (mp0) outliers start: 24 outliers final: 19 residues processed: 216 average time/residue: 0.1000 time to fit residues: 31.1387 Evaluate side-chains 208 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 406 GLN Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 104 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 406 GLN c 335 GLN c 374 HIS c 406 GLN ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.104776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081331 restraints weight = 27992.058| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.08 r_work: 0.3250 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10912 Z= 0.250 Angle : 0.960 20.647 14959 Z= 0.448 Chirality : 0.051 0.531 1903 Planarity : 0.004 0.045 1762 Dihedral : 7.464 59.927 2987 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.94 % Allowed : 16.93 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.26), residues: 1038 helix: 1.00 (0.28), residues: 356 sheet: 1.37 (0.45), residues: 129 loop : -0.24 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 282 TYR 0.017 0.002 TYR c 366 PHE 0.013 0.002 PHE C 140 TRP 0.036 0.002 TRP B 210 HIS 0.011 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00564 (10812) covalent geometry : angle 0.87733 (14679) SS BOND : bond 0.00950 ( 20) SS BOND : angle 4.47668 ( 40) hydrogen bonds : bond 0.04638 ( 425) hydrogen bonds : angle 5.01723 ( 1065) link_ALPHA1-2 : bond 0.00391 ( 3) link_ALPHA1-2 : angle 2.20388 ( 9) link_ALPHA1-3 : bond 0.01202 ( 3) link_ALPHA1-3 : angle 1.23005 ( 9) link_ALPHA1-6 : bond 0.01046 ( 3) link_ALPHA1-6 : angle 1.41935 ( 9) link_BETA1-3 : bond 0.01116 ( 1) link_BETA1-3 : angle 2.63322 ( 3) link_BETA1-4 : bond 0.00953 ( 36) link_BETA1-4 : angle 2.71583 ( 108) link_BETA1-6 : bond 0.00320 ( 1) link_BETA1-6 : angle 2.35876 ( 3) link_NAG-ASN : bond 0.00646 ( 33) link_NAG-ASN : angle 2.78838 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7809 (mp0) REVERT: A 211 ASP cc_start: 0.8124 (m-30) cc_final: 0.7622 (p0) REVERT: A 259 LEU cc_start: 0.7826 (tp) cc_final: 0.7394 (tt) REVERT: B 130 ASP cc_start: 0.8542 (t0) cc_final: 0.8261 (t0) REVERT: B 211 ASP cc_start: 0.8720 (m-30) cc_final: 0.8011 (t70) REVERT: B 214 MET cc_start: 0.8620 (mtm) cc_final: 0.8314 (ttt) REVERT: C 82 MET cc_start: 0.8553 (pmm) cc_final: 0.8144 (pmm) REVERT: C 251 ASP cc_start: 0.8819 (m-30) cc_final: 0.8575 (m-30) REVERT: a 308 GLU cc_start: 0.8331 (mp0) cc_final: 0.7908 (mt-10) REVERT: a 396 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7334 (tm-30) REVERT: b 283 TRP cc_start: 0.7547 (m100) cc_final: 0.7252 (m100) REVERT: b 289 GLU cc_start: 0.7845 (mp0) cc_final: 0.7309 (mp0) REVERT: b 295 ASN cc_start: 0.8465 (p0) cc_final: 0.8220 (p0) REVERT: b 303 GLU cc_start: 0.8620 (mp0) cc_final: 0.8220 (mp0) REVERT: b 311 ASP cc_start: 0.9193 (m-30) cc_final: 0.8936 (m-30) REVERT: b 332 MET cc_start: 0.7710 (mmm) cc_final: 0.7210 (tpt) REVERT: b 339 LYS cc_start: 0.8465 (mptt) cc_final: 0.8196 (mmtm) REVERT: b 413 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8441 (tm-30) REVERT: c 306 ASP cc_start: 0.8530 (p0) cc_final: 0.8189 (p0) outliers start: 28 outliers final: 21 residues processed: 205 average time/residue: 0.1026 time to fit residues: 30.2200 Evaluate side-chains 201 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 406 GLN Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 313 LEU Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 79 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 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 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 335 GLN b 406 GLN c 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.107660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.083803 restraints weight = 27918.898| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 4.13 r_work: 0.3302 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 10912 Z= 0.146 Angle : 0.899 20.425 14959 Z= 0.425 Chirality : 0.048 0.483 1903 Planarity : 0.003 0.046 1762 Dihedral : 7.140 59.935 2987 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.10 % Allowed : 17.98 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.26), residues: 1038 helix: 1.00 (0.29), residues: 362 sheet: 1.45 (0.46), residues: 127 loop : -0.15 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 282 TYR 0.023 0.001 TYR c 366 PHE 0.013 0.001 PHE a 262 TRP 0.035 0.001 TRP C 210 HIS 0.006 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00315 (10812) covalent geometry : angle 0.82061 (14679) SS BOND : bond 0.01028 ( 20) SS BOND : angle 4.54814 ( 40) hydrogen bonds : bond 0.04084 ( 425) hydrogen bonds : angle 4.80732 ( 1065) link_ALPHA1-2 : bond 0.00222 ( 3) link_ALPHA1-2 : angle 2.09449 ( 9) link_ALPHA1-3 : bond 0.01262 ( 3) link_ALPHA1-3 : angle 1.10472 ( 9) link_ALPHA1-6 : bond 0.01095 ( 3) link_ALPHA1-6 : angle 1.41475 ( 9) link_BETA1-3 : bond 0.01285 ( 1) link_BETA1-3 : angle 2.77265 ( 3) link_BETA1-4 : bond 0.00988 ( 36) link_BETA1-4 : angle 2.51233 ( 108) link_BETA1-6 : bond 0.00319 ( 1) link_BETA1-6 : angle 1.59645 ( 3) link_NAG-ASN : bond 0.00505 ( 33) link_NAG-ASN : angle 2.46522 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8658 (p90) cc_final: 0.8395 (p90) REVERT: A 259 LEU cc_start: 0.7755 (tp) cc_final: 0.7343 (tt) REVERT: B 70 THR cc_start: 0.8790 (p) cc_final: 0.8576 (t) REVERT: B 130 ASP cc_start: 0.8496 (t0) cc_final: 0.8190 (t0) REVERT: B 211 ASP cc_start: 0.8427 (m-30) cc_final: 0.7860 (t0) REVERT: C 233 PHE cc_start: 0.8480 (t80) cc_final: 0.8179 (t80) REVERT: C 251 ASP cc_start: 0.8784 (m-30) cc_final: 0.8548 (m-30) REVERT: a 308 GLU cc_start: 0.8223 (mp0) cc_final: 0.7847 (mt-10) REVERT: a 366 TYR cc_start: 0.8503 (m-80) cc_final: 0.8279 (m-10) REVERT: a 396 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7236 (tm-30) REVERT: b 283 TRP cc_start: 0.7385 (m100) cc_final: 0.7067 (m100) REVERT: b 289 GLU cc_start: 0.7734 (mp0) cc_final: 0.7226 (mp0) REVERT: b 295 ASN cc_start: 0.8463 (p0) cc_final: 0.8231 (p0) REVERT: b 303 GLU cc_start: 0.8595 (mp0) cc_final: 0.8255 (mp0) REVERT: b 311 ASP cc_start: 0.9125 (m-30) cc_final: 0.8892 (m-30) REVERT: b 332 MET cc_start: 0.7709 (mmm) cc_final: 0.7397 (tpt) REVERT: b 335 GLN cc_start: 0.7829 (mt0) cc_final: 0.7535 (mt0) REVERT: b 339 LYS cc_start: 0.8405 (mptt) cc_final: 0.8178 (mmtm) REVERT: b 410 MET cc_start: 0.8685 (mmm) cc_final: 0.8078 (ttm) REVERT: b 413 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8380 (tm-30) REVERT: c 306 ASP cc_start: 0.8540 (p0) cc_final: 0.8105 (p0) REVERT: c 308 GLU cc_start: 0.8083 (mp0) cc_final: 0.7879 (mp0) REVERT: c 347 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8003 (p0) outliers start: 20 outliers final: 19 residues processed: 208 average time/residue: 0.1034 time to fit residues: 30.8192 Evaluate side-chains 207 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 406 GLN Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 313 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 53 optimal weight: 0.0570 chunk 90 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 110 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN C 74 ASN ** b 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.107830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.083934 restraints weight = 28278.805| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.12 r_work: 0.3306 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10912 Z= 0.145 Angle : 0.885 20.416 14959 Z= 0.418 Chirality : 0.047 0.474 1903 Planarity : 0.003 0.046 1762 Dihedral : 6.936 58.301 2987 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.21 % Allowed : 17.35 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.26), residues: 1038 helix: 1.01 (0.29), residues: 362 sheet: 1.39 (0.46), residues: 129 loop : -0.15 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 282 TYR 0.023 0.001 TYR c 366 PHE 0.013 0.001 PHE a 262 TRP 0.036 0.001 TRP C 210 HIS 0.005 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00317 (10812) covalent geometry : angle 0.80740 (14679) SS BOND : bond 0.00916 ( 20) SS BOND : angle 4.49895 ( 40) hydrogen bonds : bond 0.04027 ( 425) hydrogen bonds : angle 4.79934 ( 1065) link_ALPHA1-2 : bond 0.00186 ( 3) link_ALPHA1-2 : angle 2.05683 ( 9) link_ALPHA1-3 : bond 0.01267 ( 3) link_ALPHA1-3 : angle 1.10067 ( 9) link_ALPHA1-6 : bond 0.01132 ( 3) link_ALPHA1-6 : angle 1.36582 ( 9) link_BETA1-3 : bond 0.01217 ( 1) link_BETA1-3 : angle 2.70002 ( 3) link_BETA1-4 : bond 0.00977 ( 36) link_BETA1-4 : angle 2.49414 ( 108) link_BETA1-6 : bond 0.00226 ( 1) link_BETA1-6 : angle 1.66063 ( 3) link_NAG-ASN : bond 0.00494 ( 33) link_NAG-ASN : angle 2.41783 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.43 seconds wall clock time: 44 minutes 57.18 seconds (2697.18 seconds total)