Starting phenix.real_space_refine on Tue May 13 15:11:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tyc_41713/05_2025/8tyc_41713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tyc_41713/05_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_41713/05_2025/8tyc_41713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tyc_41713/05_2025/8tyc_41713.map" model { file = "/net/cci-nas-00/data/ceres_data/8tyc_41713/05_2025/8tyc_41713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tyc_41713/05_2025/8tyc_41713.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.32, per 1000 atoms: 0.69 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: 3.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 2.94 Time building geometry restraints manager: 4.35 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 420 or resid 701)) selection = (chain 'b' and (resid 260 through 268 or resid 276 through 420 or resid 701)) selection = (chain 'c' and (resid 260 through 268 or resid 276 through 420 or resid 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: 1.830 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.300 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), 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 TRP 0.052 0.010 TRP C 196 HIS 0.012 0.003 HIS a 354 PHE 0.025 0.004 PHE A 233 TYR 0.063 0.009 TYR C 253 ARG 0.006 0.001 ARG A 250 Details of bonding type rmsd link_NAG-ASN : bond 0.07425 ( 33) link_NAG-ASN : angle 3.03249 ( 99) link_ALPHA1-6 : bond 0.05101 ( 3) link_ALPHA1-6 : angle 2.88869 ( 9) link_BETA1-4 : bond 0.07150 ( 36) link_BETA1-4 : angle 5.51331 ( 108) 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) hydrogen bonds : bond 0.18766 ( 425) hydrogen bonds : angle 7.37351 ( 1065) link_BETA1-6 : bond 0.04972 ( 1) link_BETA1-6 : angle 2.70987 ( 3) SS BOND : bond 0.01104 ( 20) SS BOND : angle 3.01158 ( 40) link_BETA1-3 : bond 0.10280 ( 1) link_BETA1-3 : angle 6.14907 ( 3) covalent geometry : bond 0.02115 (10812) covalent geometry : angle 1.75336 (14679) *********************** 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 : 1.059 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: 0.7979 (tp-100) REVERT: a 409 ASN cc_start: 0.8895 (m-40) cc_final: 0.8623 (m-40) REVERT: c 406 GLN cc_start: 0.8649 (tp40) cc_final: 0.8215 (tp-100) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2671 time to fit residues: 113.7390 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 : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 149 GLN C 179 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.110902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.086973 restraints weight = 26900.444| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 4.17 r_work: 0.3324 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10912 Z= 0.196 Angle : 0.956 19.710 14959 Z= 0.446 Chirality : 0.050 0.587 1903 Planarity : 0.004 0.040 1762 Dihedral : 13.136 85.034 2987 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.05 % Allowed : 10.20 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1038 helix: 0.91 (0.28), residues: 354 sheet: 2.36 (0.50), residues: 93 loop : 0.51 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 210 HIS 0.007 0.002 HIS A 141 PHE 0.018 0.002 PHE c 293 TYR 0.019 0.002 TYR A 94 ARG 0.004 0.001 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00803 ( 33) link_NAG-ASN : angle 3.15491 ( 99) link_ALPHA1-6 : bond 0.00847 ( 3) link_ALPHA1-6 : angle 1.69563 ( 9) link_BETA1-4 : bond 0.01320 ( 36) link_BETA1-4 : angle 3.94853 ( 108) link_ALPHA1-2 : bond 0.00546 ( 3) link_ALPHA1-2 : angle 2.39826 ( 9) link_ALPHA1-3 : bond 0.01666 ( 3) link_ALPHA1-3 : angle 1.35375 ( 9) hydrogen bonds : bond 0.05624 ( 425) hydrogen bonds : angle 5.70629 ( 1065) link_BETA1-6 : bond 0.00311 ( 1) link_BETA1-6 : angle 1.64855 ( 3) SS BOND : bond 0.00665 ( 20) SS BOND : angle 2.85124 ( 40) link_BETA1-3 : bond 0.01214 ( 1) link_BETA1-3 : angle 2.31578 ( 3) covalent geometry : bond 0.00415 (10812) covalent geometry : angle 0.84808 (14679) *********************** 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 243 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.7941 (mmt) cc_final: 0.7661 (mmp) REVERT: B 100 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8318 (tm-30) REVERT: C 85 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8179 (p) REVERT: C 251 ASP cc_start: 0.8725 (m-30) cc_final: 0.8252 (m-30) REVERT: a 282 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7383 (tmm-80) REVERT: a 304 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8715 (mtpp) REVERT: a 405 GLN cc_start: 0.8807 (tp40) cc_final: 0.7631 (tp-100) REVERT: a 406 GLN cc_start: 0.9324 (tp40) cc_final: 0.9099 (tp-100) REVERT: a 409 ASN cc_start: 0.9063 (m-40) cc_final: 0.8858 (m-40) REVERT: b 287 GLU cc_start: 0.9185 (pt0) cc_final: 0.8838 (pp20) REVERT: b 295 ASN cc_start: 0.8307 (p0) cc_final: 0.7930 (t0) REVERT: b 384 LYS cc_start: 0.8357 (mptt) cc_final: 0.8100 (mptt) REVERT: b 406 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8377 (mm-40) REVERT: c 289 GLU cc_start: 0.8102 (mp0) cc_final: 0.7766 (pm20) REVERT: c 304 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8590 (mtmm) REVERT: c 371 TYR cc_start: 0.8510 (p90) cc_final: 0.8199 (p90) REVERT: c 406 GLN cc_start: 0.8634 (tp40) cc_final: 0.8169 (tp-100) REVERT: c 410 MET cc_start: 0.7460 (mmm) cc_final: 0.6938 (mmm) outliers start: 29 outliers final: 12 residues processed: 225 average time/residue: 0.2311 time to fit residues: 72.6269 Evaluate side-chains 193 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 255 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain a residue 282 ARG Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain b residue 412 THR Chi-restraints excluded: chain c residue 298 VAL 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 92 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN c 354 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 = 0.3883 r_free = 0.3883 target = 0.108994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.084896 restraints weight = 27619.192| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 4.25 r_work: 0.3291 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3655 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= 0.180 Angle : 0.874 20.209 14959 Z= 0.408 Chirality : 0.050 0.544 1903 Planarity : 0.003 0.044 1762 Dihedral : 9.942 78.143 2987 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.26 % Allowed : 11.99 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1038 helix: 1.06 (0.28), residues: 362 sheet: 1.78 (0.48), residues: 116 loop : 0.09 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 210 HIS 0.006 0.001 HIS A 141 PHE 0.015 0.001 PHE c 293 TYR 0.020 0.002 TYR c 366 ARG 0.004 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 33) link_NAG-ASN : angle 2.84783 ( 99) link_ALPHA1-6 : bond 0.00782 ( 3) link_ALPHA1-6 : angle 1.68857 ( 9) link_BETA1-4 : bond 0.01125 ( 36) link_BETA1-4 : angle 3.19569 ( 108) link_ALPHA1-2 : bond 0.00272 ( 3) link_ALPHA1-2 : angle 1.98953 ( 9) link_ALPHA1-3 : bond 0.01316 ( 3) link_ALPHA1-3 : angle 0.82815 ( 9) hydrogen bonds : bond 0.04760 ( 425) hydrogen bonds : angle 5.21124 ( 1065) link_BETA1-6 : bond 0.00157 ( 1) link_BETA1-6 : angle 1.82015 ( 3) SS BOND : bond 0.01280 ( 20) SS BOND : angle 3.79311 ( 40) link_BETA1-3 : bond 0.01109 ( 1) link_BETA1-3 : angle 2.96641 ( 3) covalent geometry : bond 0.00384 (10812) covalent geometry : angle 0.77654 (14679) *********************** 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 220 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7739 (mp0) REVERT: A 211 ASP cc_start: 0.8025 (m-30) cc_final: 0.7588 (p0) REVERT: A 259 LEU cc_start: 0.7865 (tp) cc_final: 0.7587 (tt) REVERT: B 100 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8265 (tm-30) REVERT: B 192 MET cc_start: 0.9033 (tmm) cc_final: 0.8810 (tmm) REVERT: B 214 MET cc_start: 0.8648 (mtm) cc_final: 0.8425 (mtt) REVERT: C 251 ASP cc_start: 0.8777 (m-30) cc_final: 0.8320 (m-30) REVERT: a 308 GLU cc_start: 0.8228 (mp0) cc_final: 0.7544 (mt-10) REVERT: a 396 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7129 (tm-30) REVERT: a 406 GLN cc_start: 0.9392 (tp40) cc_final: 0.9096 (tp40) REVERT: a 409 ASN cc_start: 0.9289 (m-40) cc_final: 0.9018 (m-40) REVERT: b 283 TRP cc_start: 0.7731 (m100) cc_final: 0.7462 (m100) REVERT: b 287 GLU cc_start: 0.9175 (pt0) cc_final: 0.8821 (pp20) REVERT: b 304 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8583 (mtpp) REVERT: b 327 LYS cc_start: 0.7980 (ptmt) cc_final: 0.7354 (pttt) REVERT: b 352 LYS cc_start: 0.8528 (tttm) cc_final: 0.8252 (tttt) REVERT: b 384 LYS cc_start: 0.8352 (mptt) cc_final: 0.8072 (mptt) REVERT: b 401 ASP cc_start: 0.9163 (t70) cc_final: 0.8774 (t0) REVERT: b 406 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8300 (mm-40) REVERT: c 284 MET cc_start: 0.8456 (mtt) cc_final: 0.8168 (mtp) REVERT: c 304 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8504 (mtpp) REVERT: c 308 GLU cc_start: 0.8219 (mp0) cc_final: 0.7909 (mp0) REVERT: c 312 MET cc_start: 0.8932 (mmm) cc_final: 0.8598 (mmp) REVERT: c 371 TYR cc_start: 0.8606 (p90) cc_final: 0.8138 (p90) REVERT: c 406 GLN cc_start: 0.8666 (tp40) cc_final: 0.8350 (tp-100) outliers start: 31 outliers final: 15 residues processed: 207 average time/residue: 0.2187 time to fit residues: 64.2469 Evaluate side-chains 197 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 A residue 237 SER 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 282 ARG Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 263 THR 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 11 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 99 optimal weight: 0.0020 chunk 81 optimal weight: 0.0970 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- 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 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.085583 restraints weight = 27053.131| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 4.18 r_work: 0.3309 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10912 Z= 0.143 Angle : 0.817 18.619 14959 Z= 0.384 Chirality : 0.047 0.503 1903 Planarity : 0.003 0.045 1762 Dihedral : 8.339 69.495 2987 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.31 % Allowed : 13.56 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1038 helix: 1.16 (0.28), residues: 360 sheet: 1.57 (0.46), residues: 127 loop : 0.02 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 210 HIS 0.004 0.001 HIS C 141 PHE 0.011 0.001 PHE a 399 TYR 0.026 0.001 TYR c 366 ARG 0.002 0.000 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 33) link_NAG-ASN : angle 2.58582 ( 99) link_ALPHA1-6 : bond 0.00913 ( 3) link_ALPHA1-6 : angle 1.80465 ( 9) link_BETA1-4 : bond 0.01034 ( 36) link_BETA1-4 : angle 2.89264 ( 108) link_ALPHA1-2 : bond 0.00168 ( 3) link_ALPHA1-2 : angle 1.94154 ( 9) link_ALPHA1-3 : bond 0.01318 ( 3) link_ALPHA1-3 : angle 0.97301 ( 9) hydrogen bonds : bond 0.04004 ( 425) hydrogen bonds : angle 4.98483 ( 1065) link_BETA1-6 : bond 0.00246 ( 1) link_BETA1-6 : angle 1.60584 ( 3) SS BOND : bond 0.00922 ( 20) SS BOND : angle 3.98283 ( 40) link_BETA1-3 : bond 0.01134 ( 1) link_BETA1-3 : angle 2.73330 ( 3) covalent geometry : bond 0.00297 (10812) covalent geometry : angle 0.72395 (14679) *********************** 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 224 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 1.050 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: A 76 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7665 (mp0) REVERT: A 259 LEU cc_start: 0.7847 (tp) cc_final: 0.7561 (tt) REVERT: B 100 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 192 MET cc_start: 0.8990 (tmm) cc_final: 0.8781 (tmm) REVERT: C 233 PHE cc_start: 0.8307 (t80) cc_final: 0.8035 (t80) REVERT: C 251 ASP cc_start: 0.8825 (m-30) cc_final: 0.8357 (m-30) REVERT: a 304 LYS cc_start: 0.9408 (mtpp) cc_final: 0.9206 (mtpp) REVERT: a 308 GLU cc_start: 0.8179 (mp0) cc_final: 0.7500 (mt-10) REVERT: a 396 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7224 (tm-30) REVERT: a 406 GLN cc_start: 0.9395 (tp40) cc_final: 0.9074 (tp40) REVERT: a 410 MET cc_start: 0.7449 (mmm) cc_final: 0.7090 (mtp) REVERT: b 283 TRP cc_start: 0.7644 (m100) cc_final: 0.7365 (m100) REVERT: b 287 GLU cc_start: 0.9185 (pt0) cc_final: 0.8861 (pp20) REVERT: b 289 GLU cc_start: 0.7584 (mp0) cc_final: 0.7209 (mp0) REVERT: b 295 ASN cc_start: 0.8451 (p0) cc_final: 0.8178 (m-40) REVERT: b 304 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8668 (mtpp) REVERT: b 327 LYS cc_start: 0.7985 (ptmt) cc_final: 0.7542 (pttt) REVERT: b 352 LYS cc_start: 0.8513 (tttm) cc_final: 0.8240 (tttt) REVERT: b 401 ASP cc_start: 0.9162 (t70) cc_final: 0.8936 (t0) REVERT: c 308 GLU cc_start: 0.8185 (mp0) cc_final: 0.7907 (mp0) REVERT: c 371 TYR cc_start: 0.8610 (p90) cc_final: 0.8244 (p90) REVERT: c 405 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8620 (tm-30) REVERT: c 406 GLN cc_start: 0.8715 (tp40) cc_final: 0.8426 (tp40) REVERT: c 410 MET cc_start: 0.7304 (mmm) cc_final: 0.7078 (mmm) outliers start: 22 outliers final: 11 residues processed: 217 average time/residue: 0.2221 time to fit residues: 68.1138 Evaluate side-chains 202 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 C residue 199 SER 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 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 120 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 405 GLN b 305 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.108659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.084523 restraints weight = 27487.073| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.19 r_work: 0.3290 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10912 Z= 0.149 Angle : 0.824 23.070 14959 Z= 0.385 Chirality : 0.047 0.513 1903 Planarity : 0.003 0.045 1762 Dihedral : 7.741 61.941 2987 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.05 % Allowed : 14.62 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1038 helix: 1.17 (0.29), residues: 362 sheet: 1.16 (0.42), residues: 146 loop : -0.15 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 210 HIS 0.005 0.001 HIS C 141 PHE 0.010 0.001 PHE a 399 TYR 0.030 0.001 TYR c 366 ARG 0.006 0.001 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 33) link_NAG-ASN : angle 2.54065 ( 99) link_ALPHA1-6 : bond 0.00972 ( 3) link_ALPHA1-6 : angle 1.78336 ( 9) link_BETA1-4 : bond 0.00895 ( 36) link_BETA1-4 : angle 2.73903 ( 108) link_ALPHA1-2 : bond 0.00179 ( 3) link_ALPHA1-2 : angle 1.97906 ( 9) link_ALPHA1-3 : bond 0.01256 ( 3) link_ALPHA1-3 : angle 1.01041 ( 9) hydrogen bonds : bond 0.03984 ( 425) hydrogen bonds : angle 4.88609 ( 1065) link_BETA1-6 : bond 0.00118 ( 1) link_BETA1-6 : angle 1.76201 ( 3) SS BOND : bond 0.01019 ( 20) SS BOND : angle 4.01182 ( 40) link_BETA1-3 : bond 0.01099 ( 1) link_BETA1-3 : angle 2.74212 ( 3) covalent geometry : bond 0.00315 (10812) covalent geometry : angle 0.73606 (14679) *********************** 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: 29 poor density : 199 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7736 (mp0) REVERT: A 259 LEU cc_start: 0.7909 (tp) cc_final: 0.7631 (tt) REVERT: B 100 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 233 PHE cc_start: 0.8446 (t80) cc_final: 0.8095 (t80) REVERT: C 251 ASP cc_start: 0.8848 (m-30) cc_final: 0.8390 (m-30) REVERT: a 308 GLU cc_start: 0.8181 (mp0) cc_final: 0.7558 (mt-10) REVERT: a 396 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7268 (tm-30) REVERT: a 406 GLN cc_start: 0.9403 (tp40) cc_final: 0.9086 (tp40) REVERT: a 410 MET cc_start: 0.7552 (mmm) cc_final: 0.7293 (mtp) REVERT: b 283 TRP cc_start: 0.7592 (m100) cc_final: 0.7304 (m100) REVERT: b 287 GLU cc_start: 0.9220 (pt0) cc_final: 0.8855 (pp20) REVERT: b 289 GLU cc_start: 0.7697 (mp0) cc_final: 0.7295 (mp0) REVERT: b 304 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8680 (mtpp) REVERT: b 327 LYS cc_start: 0.7913 (ptmt) cc_final: 0.7484 (pttt) REVERT: b 352 LYS cc_start: 0.8480 (tttm) cc_final: 0.8209 (tttt) REVERT: b 401 ASP cc_start: 0.9148 (t70) cc_final: 0.8923 (t0) REVERT: b 406 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8262 (tp40) REVERT: c 304 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8616 (mtmm) REVERT: c 371 TYR cc_start: 0.8644 (p90) cc_final: 0.8227 (p90) REVERT: c 406 GLN cc_start: 0.8729 (tp40) cc_final: 0.8464 (tp40) REVERT: c 410 MET cc_start: 0.7599 (mmm) cc_final: 0.7044 (mmm) outliers start: 29 outliers final: 18 residues processed: 221 average time/residue: 0.2270 time to fit residues: 72.2318 Evaluate side-chains 206 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 412 THR Chi-restraints excluded: chain c residue 293 PHE 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 86 optimal weight: 3.9990 chunk 59 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN c 302 ASN ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN c 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.106204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082815 restraints weight = 27677.444| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 4.07 r_work: 0.3276 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10912 Z= 0.200 Angle : 0.886 19.068 14959 Z= 0.410 Chirality : 0.050 0.524 1903 Planarity : 0.003 0.044 1762 Dihedral : 7.715 59.367 2987 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.79 % Allowed : 14.20 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1038 helix: 1.15 (0.29), residues: 357 sheet: 1.36 (0.45), residues: 126 loop : -0.18 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 210 HIS 0.007 0.001 HIS C 141 PHE 0.011 0.001 PHE a 399 TYR 0.024 0.002 TYR c 366 ARG 0.004 0.001 ARG a 379 Details of bonding type rmsd link_NAG-ASN : bond 0.01004 ( 33) link_NAG-ASN : angle 3.10128 ( 99) link_ALPHA1-6 : bond 0.00964 ( 3) link_ALPHA1-6 : angle 1.66785 ( 9) link_BETA1-4 : bond 0.00905 ( 36) link_BETA1-4 : angle 2.73183 ( 108) link_ALPHA1-2 : bond 0.00252 ( 3) link_ALPHA1-2 : angle 2.12206 ( 9) link_ALPHA1-3 : bond 0.01192 ( 3) link_ALPHA1-3 : angle 1.13920 ( 9) hydrogen bonds : bond 0.04269 ( 425) hydrogen bonds : angle 5.00491 ( 1065) link_BETA1-6 : bond 0.00117 ( 1) link_BETA1-6 : angle 2.10351 ( 3) SS BOND : bond 0.00988 ( 20) SS BOND : angle 4.20319 ( 40) link_BETA1-3 : bond 0.01140 ( 1) link_BETA1-3 : angle 2.68501 ( 3) covalent geometry : bond 0.00439 (10812) covalent geometry : angle 0.78996 (14679) *********************** 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 229 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7786 (mp0) REVERT: A 211 ASP cc_start: 0.8055 (m-30) cc_final: 0.7554 (p0) REVERT: A 259 LEU cc_start: 0.7849 (tp) cc_final: 0.7401 (tt) REVERT: B 100 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 130 ASP cc_start: 0.8442 (t0) cc_final: 0.8222 (t0) REVERT: B 192 MET cc_start: 0.8984 (tmm) cc_final: 0.8604 (tmm) REVERT: B 250 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7812 (tmm-80) REVERT: C 82 MET cc_start: 0.8159 (ptp) cc_final: 0.7747 (pmm) REVERT: C 185 ASN cc_start: 0.7705 (t0) cc_final: 0.7493 (m-40) REVERT: C 194 MET cc_start: 0.9267 (ttm) cc_final: 0.9030 (ttm) REVERT: C 251 ASP cc_start: 0.8869 (m-30) cc_final: 0.8575 (m-30) REVERT: a 308 GLU cc_start: 0.8338 (mp0) cc_final: 0.7874 (mt-10) REVERT: a 366 TYR cc_start: 0.8576 (m-80) cc_final: 0.8313 (m-10) REVERT: a 396 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7255 (tm-30) REVERT: a 406 GLN cc_start: 0.9428 (tp40) cc_final: 0.9004 (tp40) REVERT: a 410 MET cc_start: 0.7816 (mmm) cc_final: 0.7381 (mtp) REVERT: b 283 TRP cc_start: 0.7634 (m100) cc_final: 0.7334 (m100) REVERT: b 287 GLU cc_start: 0.9255 (pt0) cc_final: 0.8903 (pp20) REVERT: b 289 GLU cc_start: 0.7772 (mp0) cc_final: 0.7323 (mp0) REVERT: b 304 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8784 (mtpp) REVERT: b 311 ASP cc_start: 0.9178 (m-30) cc_final: 0.8715 (t0) REVERT: b 327 LYS cc_start: 0.7835 (ptmt) cc_final: 0.7290 (pttt) REVERT: b 401 ASP cc_start: 0.9190 (t70) cc_final: 0.8867 (t0) REVERT: c 304 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8598 (mtmm) REVERT: c 406 GLN cc_start: 0.8734 (tp40) cc_final: 0.8460 (tp40) REVERT: c 410 MET cc_start: 0.7718 (mmm) cc_final: 0.7198 (mmm) outliers start: 36 outliers final: 25 residues processed: 218 average time/residue: 0.2114 time to fit residues: 65.3924 Evaluate side-chains 209 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 250 ARG 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 376 THR Chi-restraints excluded: chain a residue 388 VAL 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 b residue 412 THR Chi-restraints excluded: chain c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 389 SER Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 52 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 123 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 302 ASN c 305 HIS c 374 HIS ** 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 = 0.3856 r_free = 0.3856 target = 0.106505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.083055 restraints weight = 28043.549| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 4.08 r_work: 0.3279 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10912 Z= 0.167 Angle : 0.841 18.348 14959 Z= 0.395 Chirality : 0.048 0.508 1903 Planarity : 0.003 0.046 1762 Dihedral : 7.414 59.315 2987 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.15 % Allowed : 15.56 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1038 helix: 1.16 (0.29), residues: 357 sheet: 1.41 (0.46), residues: 123 loop : -0.18 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 210 HIS 0.006 0.001 HIS C 141 PHE 0.015 0.001 PHE c 399 TYR 0.022 0.001 TYR c 366 ARG 0.004 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 33) link_NAG-ASN : angle 2.63355 ( 99) link_ALPHA1-6 : bond 0.01021 ( 3) link_ALPHA1-6 : angle 1.59466 ( 9) link_BETA1-4 : bond 0.00981 ( 36) link_BETA1-4 : angle 2.62781 ( 108) link_ALPHA1-2 : bond 0.00211 ( 3) link_ALPHA1-2 : angle 2.09092 ( 9) link_ALPHA1-3 : bond 0.01258 ( 3) link_ALPHA1-3 : angle 1.10822 ( 9) hydrogen bonds : bond 0.04050 ( 425) hydrogen bonds : angle 4.92674 ( 1065) link_BETA1-6 : bond 0.00083 ( 1) link_BETA1-6 : angle 1.81750 ( 3) SS BOND : bond 0.00932 ( 20) SS BOND : angle 4.24683 ( 40) link_BETA1-3 : bond 0.01218 ( 1) link_BETA1-3 : angle 2.75848 ( 3) covalent geometry : bond 0.00365 (10812) covalent geometry : angle 0.75295 (14679) *********************** 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 223 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 1.107 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: 0.8337 (tp30) cc_final: 0.7672 (tm-30) REVERT: A 76 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7755 (mp0) REVERT: A 211 ASP cc_start: 0.8085 (m-30) cc_final: 0.7621 (p0) REVERT: A 259 LEU cc_start: 0.7815 (tp) cc_final: 0.7405 (tt) REVERT: B 100 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 130 ASP cc_start: 0.8444 (t0) cc_final: 0.8204 (t0) REVERT: B 250 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7701 (tmm-80) REVERT: C 82 MET cc_start: 0.8092 (ptp) cc_final: 0.7682 (pmm) REVERT: C 233 PHE cc_start: 0.8463 (t80) cc_final: 0.8138 (t80) REVERT: C 251 ASP cc_start: 0.8867 (m-30) cc_final: 0.8584 (m-30) REVERT: a 308 GLU cc_start: 0.8279 (mp0) cc_final: 0.7835 (mt-10) REVERT: a 366 TYR cc_start: 0.8531 (m-80) cc_final: 0.8279 (m-10) REVERT: a 396 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7292 (tm-30) REVERT: a 406 GLN cc_start: 0.9439 (tp40) cc_final: 0.9211 (tp40) REVERT: b 283 TRP cc_start: 0.7523 (m100) cc_final: 0.7212 (m100) REVERT: b 287 GLU cc_start: 0.9270 (pt0) cc_final: 0.8909 (pp20) REVERT: b 289 GLU cc_start: 0.7777 (mp0) cc_final: 0.7291 (mp0) REVERT: b 304 LYS cc_start: 0.9022 (mtpp) cc_final: 0.8664 (mtpp) REVERT: b 311 ASP cc_start: 0.9175 (m-30) cc_final: 0.8718 (t0) REVERT: b 339 LYS cc_start: 0.8368 (mptt) cc_final: 0.8148 (mmtm) REVERT: b 401 ASP cc_start: 0.9183 (t70) cc_final: 0.8854 (t0) REVERT: c 304 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8600 (mtmm) REVERT: c 406 GLN cc_start: 0.8711 (tp40) cc_final: 0.8242 (tp-100) REVERT: c 410 MET cc_start: 0.7766 (mmm) cc_final: 0.7402 (mmm) outliers start: 30 outliers final: 18 residues processed: 215 average time/residue: 0.2177 time to fit residues: 66.5297 Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 250 ARG 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 411 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** C 74 ASN c 374 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.106293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082910 restraints weight = 27555.893| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.07 r_work: 0.3280 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10912 Z= 0.169 Angle : 0.859 18.840 14959 Z= 0.401 Chirality : 0.048 0.503 1903 Planarity : 0.003 0.046 1762 Dihedral : 7.301 58.965 2987 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.73 % Allowed : 15.88 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1038 helix: 1.17 (0.28), residues: 355 sheet: 1.22 (0.44), residues: 133 loop : -0.21 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 210 HIS 0.006 0.001 HIS C 141 PHE 0.011 0.001 PHE a 399 TYR 0.019 0.001 TYR c 366 ARG 0.005 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 33) link_NAG-ASN : angle 2.63938 ( 99) link_ALPHA1-6 : bond 0.01057 ( 3) link_ALPHA1-6 : angle 1.52420 ( 9) link_BETA1-4 : bond 0.00974 ( 36) link_BETA1-4 : angle 2.60545 ( 108) link_ALPHA1-2 : bond 0.00255 ( 3) link_ALPHA1-2 : angle 2.09409 ( 9) link_ALPHA1-3 : bond 0.01223 ( 3) link_ALPHA1-3 : angle 1.10934 ( 9) hydrogen bonds : bond 0.04008 ( 425) hydrogen bonds : angle 4.87846 ( 1065) link_BETA1-6 : bond 0.00040 ( 1) link_BETA1-6 : angle 1.89400 ( 3) SS BOND : bond 0.00971 ( 20) SS BOND : angle 4.28967 ( 40) link_BETA1-3 : bond 0.01200 ( 1) link_BETA1-3 : angle 2.72372 ( 3) covalent geometry : bond 0.00371 (10812) covalent geometry : angle 0.77368 (14679) *********************** 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 217 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8318 (tp30) cc_final: 0.7707 (tm-30) REVERT: A 76 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7816 (mp0) REVERT: A 259 LEU cc_start: 0.7789 (tp) cc_final: 0.7378 (tt) REVERT: B 100 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 130 ASP cc_start: 0.8470 (t0) cc_final: 0.8223 (t0) REVERT: B 250 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7717 (tmm-80) REVERT: C 233 PHE cc_start: 0.8488 (t80) cc_final: 0.8171 (t80) REVERT: C 251 ASP cc_start: 0.8837 (m-30) cc_final: 0.8564 (m-30) REVERT: a 308 GLU cc_start: 0.8246 (mp0) cc_final: 0.7791 (mt-10) REVERT: a 366 TYR cc_start: 0.8578 (m-80) cc_final: 0.8259 (m-10) REVERT: a 396 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7244 (tm-30) REVERT: a 406 GLN cc_start: 0.9410 (tp40) cc_final: 0.9188 (tp40) REVERT: a 410 MET cc_start: 0.7493 (mtp) cc_final: 0.7253 (mtp) REVERT: b 283 TRP cc_start: 0.7462 (m100) cc_final: 0.7160 (m100) REVERT: b 287 GLU cc_start: 0.9266 (pt0) cc_final: 0.8924 (pp20) REVERT: b 289 GLU cc_start: 0.7804 (mp0) cc_final: 0.7311 (mp0) REVERT: b 304 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8692 (mtpp) REVERT: b 311 ASP cc_start: 0.9174 (m-30) cc_final: 0.8891 (m-30) REVERT: b 401 ASP cc_start: 0.9183 (t70) cc_final: 0.8854 (t0) REVERT: c 304 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8579 (mtmm) REVERT: c 306 ASP cc_start: 0.8465 (p0) cc_final: 0.8108 (p0) REVERT: c 396 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7760 (tm-30) REVERT: c 406 GLN cc_start: 0.8746 (tp40) cc_final: 0.8259 (tp-100) REVERT: c 410 MET cc_start: 0.7771 (mmm) cc_final: 0.7400 (mmm) outliers start: 26 outliers final: 21 residues processed: 210 average time/residue: 0.2074 time to fit residues: 62.0119 Evaluate side-chains 210 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 137 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 190 THR 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 214 MET Chi-restraints excluded: chain B residue 250 ARG 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 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 Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN c 374 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.107424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083463 restraints weight = 28216.136| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 4.22 r_work: 0.3296 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10912 Z= 0.142 Angle : 0.854 20.374 14959 Z= 0.401 Chirality : 0.047 0.482 1903 Planarity : 0.003 0.046 1762 Dihedral : 7.074 58.756 2987 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.31 % Allowed : 16.09 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1038 helix: 1.28 (0.29), residues: 355 sheet: 1.24 (0.44), residues: 137 loop : -0.17 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 210 HIS 0.007 0.001 HIS A 93 PHE 0.010 0.001 PHE a 262 TYR 0.018 0.001 TYR c 366 ARG 0.009 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 33) link_NAG-ASN : angle 2.53059 ( 99) link_ALPHA1-6 : bond 0.01100 ( 3) link_ALPHA1-6 : angle 1.48277 ( 9) link_BETA1-4 : bond 0.00974 ( 36) link_BETA1-4 : angle 2.52827 ( 108) link_ALPHA1-2 : bond 0.00271 ( 3) link_ALPHA1-2 : angle 2.01548 ( 9) link_ALPHA1-3 : bond 0.01285 ( 3) link_ALPHA1-3 : angle 1.08208 ( 9) hydrogen bonds : bond 0.03877 ( 425) hydrogen bonds : angle 4.81965 ( 1065) link_BETA1-6 : bond 0.00195 ( 1) link_BETA1-6 : angle 1.63897 ( 3) SS BOND : bond 0.01120 ( 20) SS BOND : angle 4.33223 ( 40) link_BETA1-3 : bond 0.01218 ( 1) link_BETA1-3 : angle 2.74707 ( 3) covalent geometry : bond 0.00299 (10812) covalent geometry : angle 0.77133 (14679) *********************** 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 218 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8291 (tp30) cc_final: 0.7673 (tm-30) REVERT: A 76 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7774 (mp0) REVERT: A 259 LEU cc_start: 0.7794 (tp) cc_final: 0.7365 (tt) REVERT: B 70 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8563 (t) REVERT: B 100 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8259 (tm-30) REVERT: B 130 ASP cc_start: 0.8446 (t0) cc_final: 0.8178 (t0) REVERT: B 192 MET cc_start: 0.9068 (tmm) cc_final: 0.8853 (tmm) REVERT: B 250 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7589 (tmm-80) REVERT: C 233 PHE cc_start: 0.8480 (t80) cc_final: 0.8156 (t80) REVERT: C 251 ASP cc_start: 0.8824 (m-30) cc_final: 0.8546 (m-30) REVERT: a 308 GLU cc_start: 0.8192 (mp0) cc_final: 0.7742 (mt-10) REVERT: a 366 TYR cc_start: 0.8551 (m-80) cc_final: 0.8207 (m-10) REVERT: a 396 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7175 (tm-30) REVERT: a 406 GLN cc_start: 0.9384 (tp40) cc_final: 0.9133 (tp40) REVERT: a 410 MET cc_start: 0.7455 (mtp) cc_final: 0.7222 (mtp) REVERT: b 283 TRP cc_start: 0.7380 (m100) cc_final: 0.7059 (m100) REVERT: b 287 GLU cc_start: 0.9253 (pt0) cc_final: 0.8927 (pp20) REVERT: b 289 GLU cc_start: 0.7759 (mp0) cc_final: 0.7270 (mp0) REVERT: b 304 LYS cc_start: 0.9172 (mtpp) cc_final: 0.8901 (mtpp) REVERT: b 311 ASP cc_start: 0.9160 (m-30) cc_final: 0.8886 (m-30) REVERT: b 339 LYS cc_start: 0.8368 (mptt) cc_final: 0.8164 (mmtm) REVERT: b 401 ASP cc_start: 0.9172 (t70) cc_final: 0.8844 (t0) REVERT: c 304 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8528 (mtmm) REVERT: c 306 ASP cc_start: 0.8351 (p0) cc_final: 0.8071 (p0) REVERT: c 396 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7743 (tm-30) REVERT: c 406 GLN cc_start: 0.8733 (tp40) cc_final: 0.8240 (tp-100) REVERT: c 410 MET cc_start: 0.7765 (mmm) cc_final: 0.7390 (mmm) outliers start: 22 outliers final: 18 residues processed: 212 average time/residue: 0.2148 time to fit residues: 64.9666 Evaluate side-chains 212 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 A residue 252 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 250 ARG 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 341 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 Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 335 GLN c 374 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.104394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.081074 restraints weight = 27971.952| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.04 r_work: 0.3246 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10912 Z= 0.230 Angle : 0.953 21.828 14959 Z= 0.445 Chirality : 0.051 0.515 1903 Planarity : 0.003 0.045 1762 Dihedral : 7.488 59.477 2987 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.63 % Allowed : 16.30 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1038 helix: 0.97 (0.28), residues: 362 sheet: 1.22 (0.45), residues: 129 loop : -0.26 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 210 HIS 0.010 0.001 HIS A 93 PHE 0.011 0.002 PHE a 262 TYR 0.017 0.001 TYR c 366 ARG 0.005 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 33) link_NAG-ASN : angle 2.75915 ( 99) link_ALPHA1-6 : bond 0.01094 ( 3) link_ALPHA1-6 : angle 1.30190 ( 9) link_BETA1-4 : bond 0.00993 ( 36) link_BETA1-4 : angle 2.67242 ( 108) link_ALPHA1-2 : bond 0.00320 ( 3) link_ALPHA1-2 : angle 2.26301 ( 9) link_ALPHA1-3 : bond 0.01125 ( 3) link_ALPHA1-3 : angle 1.21637 ( 9) hydrogen bonds : bond 0.04487 ( 425) hydrogen bonds : angle 4.96849 ( 1065) link_BETA1-6 : bond 0.00194 ( 1) link_BETA1-6 : angle 2.26433 ( 3) SS BOND : bond 0.01011 ( 20) SS BOND : angle 4.58563 ( 40) link_BETA1-3 : bond 0.01215 ( 1) link_BETA1-3 : angle 2.67904 ( 3) covalent geometry : bond 0.00514 (10812) covalent geometry : angle 0.87002 (14679) ********************** 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 215 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8306 (tp30) cc_final: 0.7671 (tm-30) REVERT: A 76 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7896 (mp0) REVERT: A 259 LEU cc_start: 0.7784 (tp) cc_final: 0.7326 (tt) REVERT: B 100 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 130 ASP cc_start: 0.8512 (t0) cc_final: 0.8269 (t0) REVERT: B 250 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7786 (tmm-80) REVERT: C 75 MET cc_start: 0.8037 (ttp) cc_final: 0.7750 (ttp) REVERT: C 194 MET cc_start: 0.9221 (ttm) cc_final: 0.8940 (mtt) REVERT: C 233 PHE cc_start: 0.8507 (t80) cc_final: 0.8180 (t80) REVERT: C 251 ASP cc_start: 0.8841 (m-30) cc_final: 0.8566 (m-30) REVERT: a 308 GLU cc_start: 0.8334 (mp0) cc_final: 0.7916 (mt-10) REVERT: a 366 TYR cc_start: 0.8640 (m-80) cc_final: 0.8311 (m-10) REVERT: a 396 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7289 (tm-30) REVERT: a 406 GLN cc_start: 0.9445 (tp40) cc_final: 0.9212 (tp40) REVERT: a 410 MET cc_start: 0.7552 (mtp) cc_final: 0.7340 (mtp) REVERT: b 283 TRP cc_start: 0.7472 (m100) cc_final: 0.7169 (m100) REVERT: b 287 GLU cc_start: 0.9293 (pt0) cc_final: 0.8958 (pp20) REVERT: b 289 GLU cc_start: 0.7846 (mp0) cc_final: 0.7340 (mp0) REVERT: b 311 ASP cc_start: 0.9200 (m-30) cc_final: 0.8956 (m-30) REVERT: b 401 ASP cc_start: 0.9192 (t70) cc_final: 0.8860 (t0) REVERT: c 300 LYS cc_start: 0.8544 (mttp) cc_final: 0.8026 (mptt) REVERT: c 304 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8585 (mtmm) REVERT: c 306 ASP cc_start: 0.8412 (p0) cc_final: 0.8115 (p0) REVERT: c 396 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7720 (tm-30) REVERT: c 406 GLN cc_start: 0.8744 (tp40) cc_final: 0.8396 (tp-100) outliers start: 25 outliers final: 20 residues processed: 210 average time/residue: 0.2153 time to fit residues: 64.3282 Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 250 ARG 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 c residue 267 SER Chi-restraints excluded: chain c residue 293 PHE Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 389 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 117 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN c 302 ASN c 374 HIS ** 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 = 0.3819 r_free = 0.3819 target = 0.104045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.080640 restraints weight = 27887.684| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 4.02 r_work: 0.3234 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 10912 Z= 0.252 Angle : 0.974 20.679 14959 Z= 0.454 Chirality : 0.051 0.519 1903 Planarity : 0.004 0.046 1762 Dihedral : 7.632 55.073 2987 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.63 % Allowed : 16.82 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1038 helix: 0.81 (0.28), residues: 363 sheet: 1.10 (0.44), residues: 136 loop : -0.30 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 210 HIS 0.010 0.001 HIS A 93 PHE 0.010 0.002 PHE a 262 TYR 0.024 0.001 TYR c 366 ARG 0.009 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 33) link_NAG-ASN : angle 2.77469 ( 99) link_ALPHA1-6 : bond 0.01091 ( 3) link_ALPHA1-6 : angle 1.20341 ( 9) link_BETA1-4 : bond 0.00961 ( 36) link_BETA1-4 : angle 2.65941 ( 108) link_ALPHA1-2 : bond 0.00410 ( 3) link_ALPHA1-2 : angle 2.22417 ( 9) link_ALPHA1-3 : bond 0.01199 ( 3) link_ALPHA1-3 : angle 1.29075 ( 9) hydrogen bonds : bond 0.04599 ( 425) hydrogen bonds : angle 5.05859 ( 1065) link_BETA1-6 : bond 0.00214 ( 1) link_BETA1-6 : angle 2.27814 ( 3) SS BOND : bond 0.01036 ( 20) SS BOND : angle 4.57858 ( 40) link_BETA1-3 : bond 0.01256 ( 1) link_BETA1-3 : angle 2.85713 ( 3) covalent geometry : bond 0.00571 (10812) covalent geometry : angle 0.89336 (14679) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4836.41 seconds wall clock time: 85 minutes 12.99 seconds (5112.99 seconds total)