Starting phenix.real_space_refine on Sat Aug 23 05:28:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejd_28178/08_2025/8ejd_28178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejd_28178/08_2025/8ejd_28178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejd_28178/08_2025/8ejd_28178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejd_28178/08_2025/8ejd_28178.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejd_28178/08_2025/8ejd_28178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejd_28178/08_2025/8ejd_28178.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 6093 2.51 5 N 1524 2.21 5 O 2094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9804 Number of models: 1 Model: "" Number of chains: 36 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1551 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "c" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1551 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "a" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1551 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "b" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "D" 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: "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: 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: "H" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 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: "W" 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: "X" 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: "Y" 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: "Z" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.63, per 1000 atoms: 0.27 Number of scatterers: 9804 At special positions: 0 Unit cell: (100.05, 98.9, 102.35, 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 2094 8.00 N 1524 7.00 C 6093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.02 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 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=2.02 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.02 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA f 3 " - " MAN f 5 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 3 " " NAG Y 1 " - " FUC Y 3 " NAG-ASN " NAG D 1 " - " ASN C 79 " " NAG E 1 " - " ASN C 89 " " NAG F 1 " - " ASN C 99 " " NAG G 1 " - " ASN C 109 " " NAG H 1 " - " ASN C 119 " " NAG I 1 " - " ASN C 167 " " NAG J 1 " - " ASN C 224 " " NAG K 1 " - " ASN c 365 " " NAG L 1 " - " ASN c 373 " " NAG M 1 " - " ASN A 79 " " NAG N 1 " - " ASN A 89 " " NAG O 1 " - " ASN A 99 " " NAG P 1 " - " ASN A 109 " " NAG Q 1 " - " ASN A 119 " " NAG R 1 " - " ASN A 167 " " NAG S 1 " - " ASN A 224 " " NAG T 1 " - " ASN a 365 " " NAG U 1 " - " ASN a 373 " " NAG V 1 " - " ASN B 79 " " NAG W 1 " - " ASN B 89 " " NAG X 1 " - " ASN B 99 " " NAG Y 1 " - " ASN B 109 " " NAG Z 1 " - " ASN B 119 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " " NAG d 1 " - " ASN B 167 " " NAG e 1 " - " ASN B 224 " " NAG f 1 " - " ASN b 365 " " NAG g 1 " - " ASN b 373 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 255.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 44.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.618A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN C 79 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 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 169 through 172 Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 205 through 213 removed outlier: 4.876A pdb=" N TRP C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 213 " --> pdb=" O TRP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 295 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 308 through 325 removed outlier: 3.814A pdb=" N MET c 312 " --> pdb=" O GLU c 308 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 345 removed outlier: 4.067A pdb=" N LYS c 339 " --> pdb=" O GLN c 335 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 424 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.619A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 79 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 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 169 through 172 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 213 removed outlier: 4.876A pdb=" N TRP A 210 " --> pdb=" O CYS A 207 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 213 " --> pdb=" O TRP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 295 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 308 through 325 removed outlier: 3.814A pdb=" N MET a 312 " --> pdb=" O GLU a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 345 removed outlier: 4.067A pdb=" N LYS a 339 " --> pdb=" O GLN a 335 " (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 424 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.619A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B 79 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 169 through 172 Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 205 through 213 removed outlier: 4.876A pdb=" N TRP B 210 " --> pdb=" O CYS B 207 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 213 " --> pdb=" O TRP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 295 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 308 through 325 removed outlier: 3.814A pdb=" N MET b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 345 removed outlier: 4.067A pdb=" N LYS b 339 " --> pdb=" O GLN b 335 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 424 Processing sheet with id=AA1, first strand: chain 'C' and resid 61 through 62 removed outlier: 9.425A pdb=" N TYR c 366 " --> pdb=" O VAL c 388 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N VAL c 388 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS c 368 " --> pdb=" O TRP c 386 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER c 392 " --> pdb=" O SER c 389 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.511A pdb=" N TYR C 219 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 277 through 280 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 62 removed outlier: 9.424A pdb=" N TYR a 366 " --> pdb=" O VAL a 388 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N VAL a 388 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS a 368 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER a 392 " --> pdb=" O SER a 389 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.511A pdb=" N TYR A 219 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 277 through 280 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 62 removed outlier: 9.425A pdb=" N TYR b 366 " --> pdb=" O VAL b 388 " (cutoff:3.500A) removed outlier: 10.869A pdb=" N VAL b 388 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS b 368 " --> pdb=" O TRP b 386 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER b 392 " --> pdb=" O SER b 389 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.511A pdb=" N TYR B 219 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 277 through 280 402 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 1.32 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: 2298 1.33 - 1.46: 3219 1.46 - 1.60: 4329 1.60 - 1.74: 6 1.74 - 1.88: 144 Bond restraints: 9996 Sorted by residual: bond pdb=" CB HIS C 93 " pdb=" CG HIS C 93 " ideal model delta sigma weight residual 1.497 1.419 0.078 1.40e-02 5.10e+03 3.07e+01 bond pdb=" CB HIS A 93 " pdb=" CG HIS A 93 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.04e+01 bond pdb=" CB HIS B 93 " pdb=" CG HIS B 93 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.02e+01 bond pdb=" CB HIS a 374 " pdb=" CG HIS a 374 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" CB HIS c 374 " pdb=" CG HIS c 374 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.40e+01 ... (remaining 9991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 12460 3.16 - 6.33: 995 6.33 - 9.49: 60 9.49 - 12.66: 12 12.66 - 15.82: 9 Bond angle restraints: 13536 Sorted by residual: angle pdb=" N GLY A 198 " pdb=" CA GLY A 198 " pdb=" C GLY A 198 " ideal model delta sigma weight residual 115.42 128.53 -13.11 1.27e+00 6.20e-01 1.07e+02 angle pdb=" N GLY C 198 " pdb=" CA GLY C 198 " pdb=" C GLY C 198 " ideal model delta sigma weight residual 115.42 128.49 -13.07 1.27e+00 6.20e-01 1.06e+02 angle pdb=" N GLY B 198 " pdb=" CA GLY B 198 " pdb=" C GLY B 198 " ideal model delta sigma weight residual 115.42 128.49 -13.07 1.27e+00 6.20e-01 1.06e+02 angle pdb=" N ILE b 345 " pdb=" CA ILE b 345 " pdb=" C ILE b 345 " ideal model delta sigma weight residual 108.58 119.35 -10.77 1.44e+00 4.82e-01 5.60e+01 angle pdb=" N ILE c 345 " pdb=" CA ILE c 345 " pdb=" C ILE c 345 " ideal model delta sigma weight residual 108.58 119.34 -10.76 1.44e+00 4.82e-01 5.59e+01 ... (remaining 13531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 6696 21.47 - 42.94: 195 42.94 - 64.41: 57 64.41 - 85.88: 84 85.88 - 107.35: 48 Dihedral angle restraints: 7080 sinusoidal: 3903 harmonic: 3177 Sorted by residual: dihedral pdb=" CB CYS A 207 " pdb=" SG CYS A 207 " pdb=" SG CYS a 360 " pdb=" CB CYS a 360 " ideal model delta sinusoidal sigma weight residual -86.00 -163.11 77.11 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS c 360 " pdb=" CB CYS c 360 " ideal model delta sinusoidal sigma weight residual -86.00 -163.10 77.10 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS b 360 " pdb=" CB CYS b 360 " ideal model delta sinusoidal sigma weight residual -86.00 -163.09 77.09 1 1.00e+01 1.00e-02 7.46e+01 ... (remaining 7077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 1608 0.309 - 0.618: 132 0.618 - 0.927: 0 0.927 - 1.236: 0 1.236 - 1.545: 3 Chirality restraints: 1743 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.25e+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 -2.70 0.30 2.00e-02 2.50e+03 2.24e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.24e+02 ... (remaining 1740 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 701 " 0.314 2.00e-02 2.50e+03 2.68e-01 8.95e+02 pdb=" C7 NAG c 701 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG c 701 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG c 701 " -0.466 2.00e-02 2.50e+03 pdb=" O7 NAG c 701 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 701 " -0.314 2.00e-02 2.50e+03 2.67e-01 8.94e+02 pdb=" C7 NAG a 701 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG a 701 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG a 701 " 0.466 2.00e-02 2.50e+03 pdb=" O7 NAG a 701 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 701 " 0.314 2.00e-02 2.50e+03 2.67e-01 8.93e+02 pdb=" C7 NAG b 701 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG b 701 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG b 701 " -0.466 2.00e-02 2.50e+03 pdb=" O7 NAG b 701 " 0.052 2.00e-02 2.50e+03 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4092 2.90 - 3.40: 9482 3.40 - 3.90: 16636 3.90 - 4.40: 19107 4.40 - 4.90: 29701 Nonbonded interactions: 79018 Sorted by model distance: nonbonded pdb=" C4 NAG K 1 " pdb=" O6 NAG K 1 " model vdw 2.400 2.776 nonbonded pdb=" C4 NAG f 1 " pdb=" O6 NAG f 1 " model vdw 2.400 2.776 nonbonded pdb=" C4 NAG T 1 " pdb=" O6 NAG T 1 " model vdw 2.400 2.776 nonbonded pdb=" OD2 ASP c 401 " pdb=" NZ LYS a 272 " model vdw 2.409 3.120 nonbonded pdb=" OD2 ASP a 401 " pdb=" NZ LYS b 272 " model vdw 2.409 3.120 ... (remaining 79013 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'T' selection = chain 'U' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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 group one per residue 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 0.111 10104 Z= 1.202 Angle : 1.929 15.821 13839 Z= 1.142 Chirality : 0.169 1.545 1743 Planarity : 0.019 0.268 1593 Dihedral : 17.205 107.346 4977 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.24), residues: 1074 helix: -0.57 (0.24), residues: 369 sheet: 1.12 (0.43), residues: 129 loop : 0.06 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 325 TYR 0.063 0.008 TYR b 363 PHE 0.024 0.005 PHE B 233 TRP 0.039 0.008 TRP A 227 HIS 0.010 0.003 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.02164 ( 9996) covalent geometry : angle 1.83171 (13536) SS BOND : bond 0.00782 ( 21) SS BOND : angle 2.68900 ( 42) hydrogen bonds : bond 0.17915 ( 402) hydrogen bonds : angle 6.44707 ( 1044) link_ALPHA1-3 : bond 0.00336 ( 3) link_ALPHA1-3 : angle 1.09254 ( 9) link_ALPHA1-6 : bond 0.05644 ( 9) link_ALPHA1-6 : angle 3.27341 ( 27) link_BETA1-4 : bond 0.07019 ( 39) link_BETA1-4 : angle 5.91989 ( 117) link_BETA1-6 : bond 0.06036 ( 3) link_BETA1-6 : angle 3.01618 ( 9) link_NAG-ASN : bond 0.07145 ( 33) link_NAG-ASN : angle 3.63699 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.327 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.7515 (m-80) cc_final: 0.7289 (m-80) REVERT: C 130 ASP cc_start: 0.8657 (t0) cc_final: 0.8383 (t0) REVERT: C 189 GLN cc_start: 0.8861 (mt0) cc_final: 0.8454 (mt0) REVERT: C 245 LEU cc_start: 0.8755 (mt) cc_final: 0.8540 (tt) REVERT: c 348 GLN cc_start: 0.8847 (mp10) cc_final: 0.8031 (mp10) REVERT: A 130 ASP cc_start: 0.8492 (t0) cc_final: 0.8286 (t0) REVERT: A 189 GLN cc_start: 0.8888 (mt0) cc_final: 0.8530 (mt0) REVERT: A 194 MET cc_start: 0.8775 (tpp) cc_final: 0.8470 (tpp) REVERT: A 245 LEU cc_start: 0.8868 (mt) cc_final: 0.8609 (tt) REVERT: a 321 GLN cc_start: 0.9343 (mm-40) cc_final: 0.9071 (mm-40) REVERT: a 348 GLN cc_start: 0.8765 (mp10) cc_final: 0.7962 (mp10) REVERT: a 405 GLN cc_start: 0.9028 (tp40) cc_final: 0.8795 (tp-100) REVERT: B 130 ASP cc_start: 0.8695 (t0) cc_final: 0.8334 (t70) REVERT: B 189 GLN cc_start: 0.9038 (mt0) cc_final: 0.8683 (mt0) REVERT: B 244 LEU cc_start: 0.9198 (mt) cc_final: 0.8500 (mt) REVERT: B 245 LEU cc_start: 0.8853 (mt) cc_final: 0.8563 (tt) REVERT: b 405 GLN cc_start: 0.8976 (tp40) cc_final: 0.8616 (tp-100) REVERT: b 409 ASN cc_start: 0.8998 (m-40) cc_final: 0.8636 (m110) REVERT: b 418 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8898 (tt0) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.1086 time to fit residues: 51.6047 Evaluate side-chains 204 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS A 170 HIS ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 324 GLN ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.097264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076189 restraints weight = 25742.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079182 restraints weight = 14400.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081282 restraints weight = 10132.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082737 restraints weight = 8084.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083721 restraints weight = 6919.554| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10104 Z= 0.205 Angle : 1.067 13.124 13839 Z= 0.498 Chirality : 0.057 0.427 1743 Planarity : 0.005 0.033 1593 Dihedral : 14.116 76.771 2934 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.59 % Allowed : 10.14 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.25), residues: 1074 helix: 0.15 (0.25), residues: 390 sheet: 0.97 (0.44), residues: 126 loop : -0.29 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 235 TYR 0.025 0.003 TYR A 62 PHE 0.012 0.002 PHE A 233 TRP 0.011 0.002 TRP c 386 HIS 0.006 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9996) covalent geometry : angle 0.93642 (13536) SS BOND : bond 0.00971 ( 21) SS BOND : angle 2.05957 ( 42) hydrogen bonds : bond 0.05872 ( 402) hydrogen bonds : angle 5.05995 ( 1044) link_ALPHA1-3 : bond 0.00917 ( 3) link_ALPHA1-3 : angle 1.71077 ( 9) link_ALPHA1-6 : bond 0.00633 ( 9) link_ALPHA1-6 : angle 1.80445 ( 27) link_BETA1-4 : bond 0.01151 ( 39) link_BETA1-4 : angle 4.50185 ( 117) link_BETA1-6 : bond 0.00321 ( 3) link_BETA1-6 : angle 1.63437 ( 9) link_NAG-ASN : bond 0.00620 ( 33) link_NAG-ASN : angle 3.46661 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.6883 (m-80) cc_final: 0.6306 (m-80) REVERT: C 66 TYR cc_start: 0.6480 (m-80) cc_final: 0.6184 (m-10) REVERT: C 80 MET cc_start: 0.9213 (mmt) cc_final: 0.8799 (tpp) REVERT: C 116 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8050 (mmtt) REVERT: C 130 ASP cc_start: 0.8399 (t0) cc_final: 0.7922 (t0) REVERT: C 189 GLN cc_start: 0.8715 (mt0) cc_final: 0.8480 (mt0) REVERT: C 194 MET cc_start: 0.9066 (tpt) cc_final: 0.8752 (tpt) REVERT: c 321 GLN cc_start: 0.9243 (mm110) cc_final: 0.8826 (mm-40) REVERT: c 351 MET cc_start: 0.9186 (mmm) cc_final: 0.8935 (mmm) REVERT: c 409 ASN cc_start: 0.9360 (m-40) cc_final: 0.8929 (m-40) REVERT: c 410 MET cc_start: 0.7675 (ttm) cc_final: 0.6720 (ttt) REVERT: c 413 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7887 (tm-30) REVERT: c 417 LYS cc_start: 0.8640 (ptmm) cc_final: 0.8096 (pttp) REVERT: A 62 TYR cc_start: 0.7000 (m-80) cc_final: 0.6779 (m-10) REVERT: A 75 MET cc_start: 0.7873 (mtt) cc_final: 0.7665 (mtm) REVERT: A 116 LYS cc_start: 0.8468 (mmtm) cc_final: 0.7634 (mmmt) REVERT: A 130 ASP cc_start: 0.8003 (t0) cc_final: 0.7749 (t0) REVERT: A 153 MET cc_start: 0.8272 (tmm) cc_final: 0.7620 (tmm) REVERT: A 194 MET cc_start: 0.9169 (tpp) cc_final: 0.8813 (tpt) REVERT: A 210 TRP cc_start: 0.7625 (t-100) cc_final: 0.7273 (t-100) REVERT: A 227 TRP cc_start: 0.8503 (t60) cc_final: 0.8124 (t60) REVERT: A 235 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7910 (ttm-80) REVERT: a 321 GLN cc_start: 0.9308 (mm-40) cc_final: 0.8736 (mm-40) REVERT: a 324 GLN cc_start: 0.8248 (tm130) cc_final: 0.7912 (tm-30) REVERT: a 374 HIS cc_start: 0.8136 (t-90) cc_final: 0.7651 (t70) REVERT: a 401 ASP cc_start: 0.7953 (p0) cc_final: 0.7734 (p0) REVERT: a 405 GLN cc_start: 0.9484 (tp40) cc_final: 0.9030 (tp-100) REVERT: a 409 ASN cc_start: 0.9202 (m-40) cc_final: 0.8887 (m-40) REVERT: a 410 MET cc_start: 0.7947 (ttm) cc_final: 0.7265 (ttm) REVERT: a 413 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8026 (tm-30) REVERT: B 66 TYR cc_start: 0.6730 (m-80) cc_final: 0.5852 (m-10) REVERT: B 116 LYS cc_start: 0.8459 (mmtt) cc_final: 0.7722 (mmmt) REVERT: B 130 ASP cc_start: 0.8239 (t0) cc_final: 0.7756 (t0) REVERT: B 134 MET cc_start: 0.8683 (tpt) cc_final: 0.8472 (tpt) REVERT: B 189 GLN cc_start: 0.8762 (mt0) cc_final: 0.8454 (mt0) REVERT: B 210 TRP cc_start: 0.7822 (t-100) cc_final: 0.7363 (t-100) REVERT: b 332 MET cc_start: 0.7776 (tpp) cc_final: 0.7550 (tpt) REVERT: b 374 HIS cc_start: 0.8325 (t-90) cc_final: 0.7923 (t-90) REVERT: b 405 GLN cc_start: 0.9472 (tp40) cc_final: 0.9188 (tp-100) REVERT: b 410 MET cc_start: 0.7795 (ttm) cc_final: 0.6776 (ttt) REVERT: b 413 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7422 (tm-30) REVERT: b 417 LYS cc_start: 0.8612 (ptmm) cc_final: 0.8051 (pttt) outliers start: 25 outliers final: 14 residues processed: 258 average time/residue: 0.0961 time to fit residues: 34.1348 Evaluate side-chains 206 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 421 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN B 209 ASN b 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.096123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075152 restraints weight = 26424.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078072 restraints weight = 15023.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.080096 restraints weight = 10637.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.081592 restraints weight = 8533.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.082591 restraints weight = 7297.660| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10104 Z= 0.182 Angle : 0.963 11.573 13839 Z= 0.448 Chirality : 0.053 0.386 1743 Planarity : 0.004 0.041 1593 Dihedral : 11.244 56.657 2934 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.05 % Favored : 93.67 % Rotamer: Outliers : 2.59 % Allowed : 12.22 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.26), residues: 1074 helix: 0.53 (0.26), residues: 390 sheet: 0.75 (0.45), residues: 126 loop : -0.39 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 325 TYR 0.021 0.002 TYR b 371 PHE 0.028 0.002 PHE A 233 TRP 0.011 0.001 TRP C 210 HIS 0.004 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9996) covalent geometry : angle 0.85158 (13536) SS BOND : bond 0.00456 ( 21) SS BOND : angle 2.77504 ( 42) hydrogen bonds : bond 0.04913 ( 402) hydrogen bonds : angle 4.60579 ( 1044) link_ALPHA1-3 : bond 0.00971 ( 3) link_ALPHA1-3 : angle 1.53470 ( 9) link_ALPHA1-6 : bond 0.00839 ( 9) link_ALPHA1-6 : angle 1.53211 ( 27) link_BETA1-4 : bond 0.01080 ( 39) link_BETA1-4 : angle 3.79454 ( 117) link_BETA1-6 : bond 0.00273 ( 3) link_BETA1-6 : angle 1.48427 ( 9) link_NAG-ASN : bond 0.00436 ( 33) link_NAG-ASN : angle 3.01060 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.256 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: symmetry clash revert: symmetry clash REVERT: C 80 MET cc_start: 0.9199 (mmt) cc_final: 0.8201 (tpp) REVERT: C 116 LYS cc_start: 0.8594 (mmtt) cc_final: 0.7707 (mmmt) REVERT: C 130 ASP cc_start: 0.8148 (t0) cc_final: 0.7660 (t0) REVERT: C 153 MET cc_start: 0.8518 (tmm) cc_final: 0.7925 (tmm) REVERT: C 194 MET cc_start: 0.9081 (tpt) cc_final: 0.8709 (tpt) REVERT: c 409 ASN cc_start: 0.9375 (m-40) cc_final: 0.8824 (m110) REVERT: c 413 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8270 (tm-30) REVERT: c 418 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8697 (tm-30) REVERT: A 62 TYR cc_start: 0.6943 (m-80) cc_final: 0.6719 (m-80) REVERT: A 66 TYR cc_start: 0.6815 (m-80) cc_final: 0.5640 (m-10) REVERT: A 75 MET cc_start: 0.7914 (mtt) cc_final: 0.7609 (mtm) REVERT: A 116 LYS cc_start: 0.8544 (mmtm) cc_final: 0.7638 (mmmt) REVERT: A 130 ASP cc_start: 0.8236 (t0) cc_final: 0.7990 (t0) REVERT: A 153 MET cc_start: 0.8378 (tmm) cc_final: 0.7615 (tmm) REVERT: A 189 GLN cc_start: 0.8807 (mt0) cc_final: 0.8478 (mm-40) REVERT: A 227 TRP cc_start: 0.8445 (t60) cc_final: 0.7960 (t60) REVERT: A 235 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7400 (ttm-80) REVERT: a 287 GLU cc_start: 0.7571 (tp30) cc_final: 0.6750 (tp30) REVERT: a 321 GLN cc_start: 0.9304 (mm-40) cc_final: 0.9037 (mm110) REVERT: a 324 GLN cc_start: 0.8290 (tm130) cc_final: 0.7662 (tm-30) REVERT: a 341 VAL cc_start: 0.9429 (t) cc_final: 0.9223 (t) REVERT: a 351 MET cc_start: 0.9101 (tpp) cc_final: 0.8396 (mmm) REVERT: a 374 HIS cc_start: 0.8476 (t-90) cc_final: 0.8093 (t-90) REVERT: a 405 GLN cc_start: 0.9532 (tp40) cc_final: 0.9018 (tp-100) REVERT: a 409 ASN cc_start: 0.9342 (m-40) cc_final: 0.8941 (m-40) REVERT: a 410 MET cc_start: 0.8022 (ttm) cc_final: 0.7208 (ptm) REVERT: a 413 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 62 TYR cc_start: 0.6912 (m-80) cc_final: 0.6529 (m-80) REVERT: B 75 MET cc_start: 0.7553 (mtm) cc_final: 0.7297 (mtm) REVERT: B 116 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7489 (mmmt) REVERT: B 130 ASP cc_start: 0.8201 (t0) cc_final: 0.7625 (t0) REVERT: B 134 MET cc_start: 0.8724 (tpt) cc_final: 0.8309 (tmm) REVERT: B 189 GLN cc_start: 0.8777 (mt0) cc_final: 0.7962 (mt0) REVERT: B 210 TRP cc_start: 0.7668 (t-100) cc_final: 0.6607 (t-100) REVERT: b 303 GLU cc_start: 0.7921 (tp30) cc_final: 0.7645 (tp30) REVERT: b 357 ASP cc_start: 0.8888 (t70) cc_final: 0.8688 (t0) REVERT: b 374 HIS cc_start: 0.8366 (t-90) cc_final: 0.8056 (t-90) REVERT: b 405 GLN cc_start: 0.9520 (tp40) cc_final: 0.9241 (tp-100) REVERT: b 409 ASN cc_start: 0.9417 (m-40) cc_final: 0.9184 (m110) REVERT: b 414 MET cc_start: 0.8104 (tmm) cc_final: 0.7679 (ttm) REVERT: b 418 GLU cc_start: 0.9187 (tt0) cc_final: 0.8711 (mt-10) outliers start: 25 outliers final: 14 residues processed: 230 average time/residue: 0.0864 time to fit residues: 27.7301 Evaluate side-chains 204 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 55 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 416 GLN B 90 ASN B 115 HIS B 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.096412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.075225 restraints weight = 26972.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078188 restraints weight = 15336.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.080208 restraints weight = 10886.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.081680 restraints weight = 8750.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082683 restraints weight = 7521.862| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10104 Z= 0.151 Angle : 0.886 11.425 13839 Z= 0.410 Chirality : 0.050 0.380 1743 Planarity : 0.004 0.045 1593 Dihedral : 9.249 52.422 2934 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.28 % Allowed : 13.46 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.26), residues: 1074 helix: 0.39 (0.26), residues: 411 sheet: 0.61 (0.45), residues: 126 loop : -0.34 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 325 TYR 0.019 0.001 TYR b 371 PHE 0.023 0.002 PHE A 233 TRP 0.011 0.001 TRP c 386 HIS 0.004 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9996) covalent geometry : angle 0.78185 (13536) SS BOND : bond 0.00472 ( 21) SS BOND : angle 2.79770 ( 42) hydrogen bonds : bond 0.04345 ( 402) hydrogen bonds : angle 4.28921 ( 1044) link_ALPHA1-3 : bond 0.01169 ( 3) link_ALPHA1-3 : angle 1.47791 ( 9) link_ALPHA1-6 : bond 0.00748 ( 9) link_ALPHA1-6 : angle 1.56845 ( 27) link_BETA1-4 : bond 0.00841 ( 39) link_BETA1-4 : angle 3.38806 ( 117) link_BETA1-6 : bond 0.00335 ( 3) link_BETA1-6 : angle 1.39219 ( 9) link_NAG-ASN : bond 0.00384 ( 33) link_NAG-ASN : angle 2.87988 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6311 (m-10) cc_final: 0.5900 (m-10) REVERT: C 116 LYS cc_start: 0.8643 (mmtt) cc_final: 0.7731 (mmmt) REVERT: C 130 ASP cc_start: 0.8069 (t0) cc_final: 0.7555 (t0) REVERT: C 153 MET cc_start: 0.8592 (tmm) cc_final: 0.7982 (tmm) REVERT: c 303 GLU cc_start: 0.7732 (tp30) cc_final: 0.7462 (tp30) REVERT: c 410 MET cc_start: 0.7781 (ttm) cc_final: 0.6738 (ttm) REVERT: c 413 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8294 (tm-30) REVERT: c 418 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8933 (mt-10) REVERT: A 66 TYR cc_start: 0.6654 (m-80) cc_final: 0.5840 (m-10) REVERT: A 116 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8211 (mmtt) REVERT: A 130 ASP cc_start: 0.8298 (t0) cc_final: 0.8031 (t0) REVERT: A 153 MET cc_start: 0.8516 (tmm) cc_final: 0.7721 (tmm) REVERT: A 189 GLN cc_start: 0.8759 (mt0) cc_final: 0.8347 (mm-40) REVERT: A 194 MET cc_start: 0.9145 (tpp) cc_final: 0.8662 (tpp) REVERT: A 227 TRP cc_start: 0.8422 (t60) cc_final: 0.8077 (t60) REVERT: A 235 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7461 (ttm-80) REVERT: a 303 GLU cc_start: 0.7906 (tp30) cc_final: 0.7706 (tp30) REVERT: a 321 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9026 (mm110) REVERT: a 324 GLN cc_start: 0.8324 (tm130) cc_final: 0.7675 (tm-30) REVERT: a 374 HIS cc_start: 0.8345 (t-90) cc_final: 0.7925 (t-90) REVERT: a 405 GLN cc_start: 0.9537 (tp40) cc_final: 0.9176 (tp-100) REVERT: a 409 ASN cc_start: 0.9361 (m-40) cc_final: 0.9020 (m110) REVERT: a 410 MET cc_start: 0.8014 (ttm) cc_final: 0.7114 (ttt) REVERT: a 413 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 62 TYR cc_start: 0.6843 (m-80) cc_final: 0.6557 (m-80) REVERT: B 116 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7407 (mmmt) REVERT: B 130 ASP cc_start: 0.8289 (t0) cc_final: 0.7721 (t0) REVERT: b 270 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6940 (mm-30) REVERT: b 303 GLU cc_start: 0.7929 (tp30) cc_final: 0.7533 (tp30) REVERT: b 374 HIS cc_start: 0.8376 (t-90) cc_final: 0.7887 (t-90) REVERT: b 405 GLN cc_start: 0.9529 (tp40) cc_final: 0.9299 (tp-100) REVERT: b 413 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8018 (tm-30) REVERT: b 418 GLU cc_start: 0.9194 (tt0) cc_final: 0.8924 (tm-30) outliers start: 22 outliers final: 9 residues processed: 217 average time/residue: 0.0882 time to fit residues: 26.9046 Evaluate side-chains 196 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 185 ASN ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN A 90 ASN a 416 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 335 GLN b 416 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.094132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072977 restraints weight = 26869.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075826 restraints weight = 15309.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077791 restraints weight = 10937.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079166 restraints weight = 8796.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080105 restraints weight = 7622.258| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.004 0.038 10104 Z= 0.193 Angle : 0.877 10.619 13839 Z= 0.405 Chirality : 0.049 0.383 1743 Planarity : 0.004 0.045 1593 Dihedral : 8.734 51.883 2934 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.42 % Allowed : 14.49 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.26), residues: 1074 helix: 0.59 (0.27), residues: 408 sheet: 0.69 (0.53), residues: 96 loop : -0.59 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 248 TYR 0.020 0.002 TYR b 371 PHE 0.013 0.002 PHE B 233 TRP 0.015 0.001 TRP a 386 HIS 0.006 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9996) covalent geometry : angle 0.77789 (13536) SS BOND : bond 0.00468 ( 21) SS BOND : angle 2.40597 ( 42) hydrogen bonds : bond 0.04361 ( 402) hydrogen bonds : angle 4.21985 ( 1044) link_ALPHA1-3 : bond 0.01048 ( 3) link_ALPHA1-3 : angle 1.66545 ( 9) link_ALPHA1-6 : bond 0.00657 ( 9) link_ALPHA1-6 : angle 1.59433 ( 27) link_BETA1-4 : bond 0.00768 ( 39) link_BETA1-4 : angle 3.21924 ( 117) link_BETA1-6 : bond 0.00174 ( 3) link_BETA1-6 : angle 1.64600 ( 9) link_NAG-ASN : bond 0.00320 ( 33) link_NAG-ASN : angle 2.96491 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.360 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: C 116 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8131 (mmmt) REVERT: C 130 ASP cc_start: 0.8262 (t0) cc_final: 0.7658 (t0) REVERT: C 153 MET cc_start: 0.8543 (tmm) cc_final: 0.7942 (tmm) REVERT: c 349 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9214 (tp) REVERT: c 413 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8329 (tm-30) REVERT: c 418 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8733 (tm-30) REVERT: A 66 TYR cc_start: 0.6702 (m-80) cc_final: 0.5750 (m-10) REVERT: A 116 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8190 (mmtt) REVERT: A 130 ASP cc_start: 0.7994 (t0) cc_final: 0.7633 (t0) REVERT: A 153 MET cc_start: 0.8552 (tmm) cc_final: 0.7708 (tmm) REVERT: A 189 GLN cc_start: 0.8737 (mt0) cc_final: 0.8272 (mt0) REVERT: A 194 MET cc_start: 0.9253 (tpp) cc_final: 0.8759 (tpt) REVERT: A 250 ARG cc_start: 0.7352 (mmt180) cc_final: 0.7140 (mmt180) REVERT: a 324 GLN cc_start: 0.8381 (tm130) cc_final: 0.8032 (tm-30) REVERT: a 341 VAL cc_start: 0.9374 (t) cc_final: 0.9171 (t) REVERT: a 374 HIS cc_start: 0.8461 (t-90) cc_final: 0.8037 (t-90) REVERT: a 405 GLN cc_start: 0.9545 (tp40) cc_final: 0.9299 (tp-100) REVERT: a 410 MET cc_start: 0.8079 (ttm) cc_final: 0.7184 (ttt) REVERT: a 413 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 116 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7415 (mmmt) REVERT: B 125 LYS cc_start: 0.9028 (mmtm) cc_final: 0.8793 (mmtm) REVERT: B 130 ASP cc_start: 0.8339 (t0) cc_final: 0.7869 (t0) REVERT: B 189 GLN cc_start: 0.8630 (mt0) cc_final: 0.8204 (mm-40) REVERT: B 214 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8665 (mtm) REVERT: b 303 GLU cc_start: 0.7953 (tp30) cc_final: 0.7530 (tp30) REVERT: b 374 HIS cc_start: 0.8410 (t-90) cc_final: 0.7927 (t-90) REVERT: b 405 GLN cc_start: 0.9533 (tp40) cc_final: 0.9246 (tp-100) REVERT: b 409 ASN cc_start: 0.9449 (m-40) cc_final: 0.9224 (m110) REVERT: b 413 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8169 (tm-30) REVERT: b 418 GLU cc_start: 0.9157 (tt0) cc_final: 0.8935 (tm-30) outliers start: 33 outliers final: 15 residues processed: 210 average time/residue: 0.0941 time to fit residues: 27.4792 Evaluate side-chains 197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 HIS ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN A 247 GLN ** B 90 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 = 0.3618 r_free = 0.3618 target = 0.094581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074562 restraints weight = 27655.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077005 restraints weight = 17277.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078777 restraints weight = 12937.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079985 restraints weight = 10691.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.080802 restraints weight = 9393.356| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10104 Z= 0.201 Angle : 0.871 10.486 13839 Z= 0.402 Chirality : 0.049 0.398 1743 Planarity : 0.004 0.061 1593 Dihedral : 8.575 51.917 2934 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.48 % Allowed : 16.56 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.26), residues: 1074 helix: 0.93 (0.27), residues: 387 sheet: 0.47 (0.51), residues: 96 loop : -0.71 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 248 TYR 0.017 0.002 TYR b 371 PHE 0.011 0.002 PHE B 157 TRP 0.016 0.001 TRP a 386 HIS 0.006 0.001 HIS C 93 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9996) covalent geometry : angle 0.77997 (13536) SS BOND : bond 0.00396 ( 21) SS BOND : angle 1.52471 ( 42) hydrogen bonds : bond 0.04327 ( 402) hydrogen bonds : angle 4.24188 ( 1044) link_ALPHA1-3 : bond 0.01028 ( 3) link_ALPHA1-3 : angle 1.54875 ( 9) link_ALPHA1-6 : bond 0.00642 ( 9) link_ALPHA1-6 : angle 1.59281 ( 27) link_BETA1-4 : bond 0.00763 ( 39) link_BETA1-4 : angle 3.13123 ( 117) link_BETA1-6 : bond 0.00123 ( 3) link_BETA1-6 : angle 1.79048 ( 9) link_NAG-ASN : bond 0.00300 ( 33) link_NAG-ASN : angle 3.01571 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7784 (mmmt) REVERT: C 130 ASP cc_start: 0.8445 (t0) cc_final: 0.7912 (t0) REVERT: C 153 MET cc_start: 0.8566 (tmm) cc_final: 0.8003 (tmm) REVERT: c 349 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9282 (tp) REVERT: c 351 MET cc_start: 0.9037 (mmm) cc_final: 0.8767 (mmm) REVERT: c 413 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 66 TYR cc_start: 0.6931 (m-80) cc_final: 0.5902 (m-10) REVERT: A 116 LYS cc_start: 0.8323 (mmtm) cc_final: 0.7746 (mmtt) REVERT: A 130 ASP cc_start: 0.8266 (t0) cc_final: 0.7963 (t70) REVERT: A 153 MET cc_start: 0.8577 (tmm) cc_final: 0.8201 (tmm) REVERT: A 189 GLN cc_start: 0.8720 (mt0) cc_final: 0.8312 (mt0) REVERT: A 194 MET cc_start: 0.9099 (tpp) cc_final: 0.8857 (tpt) REVERT: A 235 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.7820 (ttm-80) REVERT: a 287 GLU cc_start: 0.7074 (tp30) cc_final: 0.6583 (tp30) REVERT: a 351 MET cc_start: 0.9172 (tpp) cc_final: 0.8882 (mmm) REVERT: a 374 HIS cc_start: 0.8283 (t-90) cc_final: 0.8005 (t-90) REVERT: a 410 MET cc_start: 0.8054 (ttm) cc_final: 0.7105 (ttt) REVERT: a 413 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8091 (tm-30) REVERT: B 116 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7121 (mmmt) REVERT: B 125 LYS cc_start: 0.9063 (mmtm) cc_final: 0.8831 (mmtm) REVERT: B 130 ASP cc_start: 0.8562 (t0) cc_final: 0.8250 (t0) REVERT: B 189 GLN cc_start: 0.8596 (mt0) cc_final: 0.8267 (mm-40) REVERT: b 303 GLU cc_start: 0.7989 (tp30) cc_final: 0.7576 (tp30) REVERT: b 347 ASP cc_start: 0.8189 (t70) cc_final: 0.7908 (t70) REVERT: b 374 HIS cc_start: 0.8153 (t-90) cc_final: 0.7831 (t70) REVERT: b 405 GLN cc_start: 0.9366 (tp40) cc_final: 0.9152 (tp-100) REVERT: b 413 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8081 (tm-30) outliers start: 24 outliers final: 15 residues processed: 198 average time/residue: 0.0930 time to fit residues: 25.6879 Evaluate side-chains 191 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.0010 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 84 optimal weight: 0.0170 overall best weight: 0.5026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.096537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.076583 restraints weight = 27605.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.079227 restraints weight = 17046.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.081121 restraints weight = 12534.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.082432 restraints weight = 10230.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.083260 restraints weight = 8889.497| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10104 Z= 0.141 Angle : 0.818 10.179 13839 Z= 0.380 Chirality : 0.046 0.395 1743 Planarity : 0.003 0.045 1593 Dihedral : 8.151 51.960 2934 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.17 % Allowed : 17.60 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.26), residues: 1074 helix: 0.86 (0.27), residues: 387 sheet: 0.56 (0.54), residues: 96 loop : -0.67 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 248 TYR 0.021 0.001 TYR b 371 PHE 0.012 0.001 PHE B 233 TRP 0.010 0.001 TRP C 210 HIS 0.004 0.001 HIS c 305 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9996) covalent geometry : angle 0.73399 (13536) SS BOND : bond 0.00298 ( 21) SS BOND : angle 1.29751 ( 42) hydrogen bonds : bond 0.03908 ( 402) hydrogen bonds : angle 4.17288 ( 1044) link_ALPHA1-3 : bond 0.01211 ( 3) link_ALPHA1-3 : angle 1.12729 ( 9) link_ALPHA1-6 : bond 0.00680 ( 9) link_ALPHA1-6 : angle 1.44292 ( 27) link_BETA1-4 : bond 0.00784 ( 39) link_BETA1-4 : angle 2.99000 ( 117) link_BETA1-6 : bond 0.00326 ( 3) link_BETA1-6 : angle 1.44106 ( 9) link_NAG-ASN : bond 0.00331 ( 33) link_NAG-ASN : angle 2.76850 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7822 (mmmt) REVERT: C 130 ASP cc_start: 0.8370 (t0) cc_final: 0.7833 (t0) REVERT: C 153 MET cc_start: 0.8550 (tmm) cc_final: 0.8012 (tmm) REVERT: c 351 MET cc_start: 0.9008 (mmm) cc_final: 0.8722 (mmm) REVERT: c 413 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8260 (tm-30) REVERT: c 414 MET cc_start: 0.8234 (tmm) cc_final: 0.7940 (ttm) REVERT: c 415 LEU cc_start: 0.9274 (tp) cc_final: 0.8950 (tp) REVERT: A 116 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7747 (mmtt) REVERT: A 130 ASP cc_start: 0.8129 (t0) cc_final: 0.7803 (t0) REVERT: A 153 MET cc_start: 0.8581 (tmm) cc_final: 0.7815 (tmm) REVERT: A 189 GLN cc_start: 0.8767 (mt0) cc_final: 0.8343 (mm-40) REVERT: A 235 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7722 (ttm-80) REVERT: a 287 GLU cc_start: 0.7246 (tp30) cc_final: 0.6782 (tp30) REVERT: a 351 MET cc_start: 0.9118 (tpp) cc_final: 0.8791 (mmm) REVERT: a 374 HIS cc_start: 0.8155 (t-90) cc_final: 0.7845 (t-90) REVERT: a 410 MET cc_start: 0.7962 (ttm) cc_final: 0.7529 (ttm) REVERT: a 413 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8167 (tm-30) REVERT: B 66 TYR cc_start: 0.6666 (m-80) cc_final: 0.6087 (m-10) REVERT: B 116 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7121 (mmmt) REVERT: B 130 ASP cc_start: 0.8504 (t0) cc_final: 0.8189 (t0) REVERT: B 189 GLN cc_start: 0.8661 (mt0) cc_final: 0.8274 (mm-40) REVERT: b 347 ASP cc_start: 0.8045 (t70) cc_final: 0.7598 (t70) REVERT: b 374 HIS cc_start: 0.8028 (t-90) cc_final: 0.7827 (t70) REVERT: b 410 MET cc_start: 0.7911 (ttm) cc_final: 0.6973 (ttt) REVERT: b 413 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8120 (tm-30) outliers start: 21 outliers final: 13 residues processed: 196 average time/residue: 0.0967 time to fit residues: 26.1249 Evaluate side-chains 187 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 419 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN b 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.096312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076443 restraints weight = 27486.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079023 restraints weight = 16828.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.080919 restraints weight = 12425.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082184 restraints weight = 10156.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.083092 restraints weight = 8844.142| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10104 Z= 0.149 Angle : 0.823 9.996 13839 Z= 0.384 Chirality : 0.046 0.381 1743 Planarity : 0.004 0.050 1593 Dihedral : 7.967 52.530 2934 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.38 % Allowed : 18.12 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.26), residues: 1074 helix: 0.96 (0.27), residues: 387 sheet: 0.59 (0.54), residues: 96 loop : -0.68 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 248 TYR 0.026 0.001 TYR a 371 PHE 0.011 0.001 PHE B 233 TRP 0.021 0.001 TRP C 210 HIS 0.005 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9996) covalent geometry : angle 0.74188 (13536) SS BOND : bond 0.00281 ( 21) SS BOND : angle 1.21888 ( 42) hydrogen bonds : bond 0.03969 ( 402) hydrogen bonds : angle 4.10671 ( 1044) link_ALPHA1-3 : bond 0.01049 ( 3) link_ALPHA1-3 : angle 1.26182 ( 9) link_ALPHA1-6 : bond 0.00639 ( 9) link_ALPHA1-6 : angle 1.44346 ( 27) link_BETA1-4 : bond 0.00746 ( 39) link_BETA1-4 : angle 2.93120 ( 117) link_BETA1-6 : bond 0.00268 ( 3) link_BETA1-6 : angle 1.43796 ( 9) link_NAG-ASN : bond 0.00310 ( 33) link_NAG-ASN : angle 2.77195 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7815 (mmmt) REVERT: C 130 ASP cc_start: 0.8350 (t0) cc_final: 0.7816 (t0) REVERT: C 153 MET cc_start: 0.8510 (tmm) cc_final: 0.7961 (tmm) REVERT: c 351 MET cc_start: 0.8986 (mmm) cc_final: 0.8726 (mmm) REVERT: c 410 MET cc_start: 0.7832 (ttm) cc_final: 0.7041 (ttm) REVERT: c 413 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 130 ASP cc_start: 0.8106 (t0) cc_final: 0.7769 (t0) REVERT: A 153 MET cc_start: 0.8591 (tmm) cc_final: 0.7810 (tmm) REVERT: A 189 GLN cc_start: 0.8761 (mt0) cc_final: 0.8344 (mm-40) REVERT: A 235 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.7829 (ttm-80) REVERT: a 287 GLU cc_start: 0.7207 (tp30) cc_final: 0.6736 (tp30) REVERT: a 351 MET cc_start: 0.9107 (tpp) cc_final: 0.8811 (mmm) REVERT: a 374 HIS cc_start: 0.8158 (t-90) cc_final: 0.7840 (t-90) REVERT: a 401 ASP cc_start: 0.7479 (p0) cc_final: 0.7154 (p0) REVERT: a 410 MET cc_start: 0.7978 (ttm) cc_final: 0.7537 (ttm) REVERT: a 413 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8177 (tm-30) REVERT: B 116 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7105 (mmmt) REVERT: B 125 LYS cc_start: 0.9026 (mmtm) cc_final: 0.8788 (mmtm) REVERT: B 130 ASP cc_start: 0.8504 (t0) cc_final: 0.8148 (t0) REVERT: B 189 GLN cc_start: 0.8627 (mt0) cc_final: 0.8223 (mm-40) REVERT: b 347 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7372 (t70) REVERT: b 348 GLN cc_start: 0.8693 (mp10) cc_final: 0.8221 (mm110) REVERT: b 374 HIS cc_start: 0.8080 (t-90) cc_final: 0.7747 (t-90) REVERT: b 413 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8173 (tm-30) outliers start: 23 outliers final: 17 residues processed: 198 average time/residue: 0.1001 time to fit residues: 27.3773 Evaluate side-chains 192 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 419 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.0000 chunk 53 optimal weight: 0.5980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN B 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.096244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076402 restraints weight = 27512.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078950 restraints weight = 17085.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080789 restraints weight = 12664.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.082044 restraints weight = 10399.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.082841 restraints weight = 9074.245| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10104 Z= 0.161 Angle : 0.849 9.875 13839 Z= 0.396 Chirality : 0.046 0.379 1743 Planarity : 0.004 0.044 1593 Dihedral : 7.864 52.927 2934 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.07 % Allowed : 18.74 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.26), residues: 1074 helix: 0.93 (0.27), residues: 387 sheet: 0.01 (0.54), residues: 102 loop : -0.62 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 248 TYR 0.025 0.001 TYR B 62 PHE 0.009 0.001 PHE B 233 TRP 0.023 0.001 TRP C 210 HIS 0.005 0.001 HIS C 93 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9996) covalent geometry : angle 0.77130 (13536) SS BOND : bond 0.00280 ( 21) SS BOND : angle 1.25764 ( 42) hydrogen bonds : bond 0.03941 ( 402) hydrogen bonds : angle 4.10039 ( 1044) link_ALPHA1-3 : bond 0.01008 ( 3) link_ALPHA1-3 : angle 1.20477 ( 9) link_ALPHA1-6 : bond 0.00633 ( 9) link_ALPHA1-6 : angle 1.45802 ( 27) link_BETA1-4 : bond 0.00737 ( 39) link_BETA1-4 : angle 2.89629 ( 117) link_BETA1-6 : bond 0.00240 ( 3) link_BETA1-6 : angle 1.46592 ( 9) link_NAG-ASN : bond 0.00349 ( 33) link_NAG-ASN : angle 2.79826 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7812 (mmmt) REVERT: C 130 ASP cc_start: 0.8352 (t0) cc_final: 0.7835 (t0) REVERT: C 153 MET cc_start: 0.8485 (tmm) cc_final: 0.7934 (tmm) REVERT: C 248 ARG cc_start: 0.7131 (tpt170) cc_final: 0.6625 (tpm170) REVERT: c 351 MET cc_start: 0.8989 (mmm) cc_final: 0.8747 (mmm) REVERT: c 413 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 116 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7647 (mmtt) REVERT: A 130 ASP cc_start: 0.8171 (t0) cc_final: 0.7856 (t70) REVERT: A 153 MET cc_start: 0.8612 (tmm) cc_final: 0.7835 (tmm) REVERT: A 189 GLN cc_start: 0.8773 (mt0) cc_final: 0.8368 (mm-40) REVERT: A 235 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7832 (ttm-80) REVERT: a 287 GLU cc_start: 0.7220 (tp30) cc_final: 0.6803 (tp30) REVERT: a 332 MET cc_start: 0.7485 (tpp) cc_final: 0.7079 (mmm) REVERT: a 351 MET cc_start: 0.9109 (tpp) cc_final: 0.8804 (mmm) REVERT: a 374 HIS cc_start: 0.8137 (t-90) cc_final: 0.7835 (t-90) REVERT: a 410 MET cc_start: 0.8003 (ttm) cc_final: 0.7565 (ttm) REVERT: a 413 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8189 (tm-30) REVERT: B 116 LYS cc_start: 0.7840 (mmtt) cc_final: 0.7147 (mmmt) REVERT: B 130 ASP cc_start: 0.8468 (t0) cc_final: 0.8163 (t0) REVERT: b 374 HIS cc_start: 0.8044 (t-90) cc_final: 0.7727 (t-90) REVERT: b 418 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8723 (tm-30) outliers start: 20 outliers final: 16 residues processed: 191 average time/residue: 0.0981 time to fit residues: 25.8229 Evaluate side-chains 183 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 345 ILE Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.077158 restraints weight = 27407.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079787 restraints weight = 16920.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081641 restraints weight = 12461.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.082908 restraints weight = 10206.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.083779 restraints weight = 8894.245| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10104 Z= 0.149 Angle : 0.846 9.735 13839 Z= 0.394 Chirality : 0.046 0.376 1743 Planarity : 0.004 0.043 1593 Dihedral : 7.715 53.184 2934 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.66 % Allowed : 19.15 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.26), residues: 1074 helix: 0.99 (0.27), residues: 387 sheet: 0.02 (0.55), residues: 102 loop : -0.62 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 248 TYR 0.028 0.001 TYR B 62 PHE 0.009 0.001 PHE B 233 TRP 0.025 0.001 TRP C 210 HIS 0.006 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9996) covalent geometry : angle 0.77137 (13536) SS BOND : bond 0.00313 ( 21) SS BOND : angle 1.24847 ( 42) hydrogen bonds : bond 0.03862 ( 402) hydrogen bonds : angle 4.11971 ( 1044) link_ALPHA1-3 : bond 0.00980 ( 3) link_ALPHA1-3 : angle 1.18396 ( 9) link_ALPHA1-6 : bond 0.00633 ( 9) link_ALPHA1-6 : angle 1.42668 ( 27) link_BETA1-4 : bond 0.00737 ( 39) link_BETA1-4 : angle 2.87609 ( 117) link_BETA1-6 : bond 0.00267 ( 3) link_BETA1-6 : angle 1.43560 ( 9) link_NAG-ASN : bond 0.00320 ( 33) link_NAG-ASN : angle 2.71074 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7789 (mmmt) REVERT: C 130 ASP cc_start: 0.8376 (t0) cc_final: 0.7846 (t0) REVERT: C 153 MET cc_start: 0.8531 (tmm) cc_final: 0.7981 (tmm) REVERT: c 403 ILE cc_start: 0.8319 (pt) cc_final: 0.8110 (tp) REVERT: c 410 MET cc_start: 0.7886 (ttm) cc_final: 0.7072 (ttm) REVERT: c 413 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 116 LYS cc_start: 0.8324 (mmtm) cc_final: 0.7647 (mmtt) REVERT: A 130 ASP cc_start: 0.8188 (t0) cc_final: 0.7865 (t70) REVERT: A 153 MET cc_start: 0.8598 (tmm) cc_final: 0.7840 (tmm) REVERT: A 235 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7867 (ttm-80) REVERT: a 287 GLU cc_start: 0.7225 (tp30) cc_final: 0.6833 (tp30) REVERT: a 351 MET cc_start: 0.9116 (tpp) cc_final: 0.8825 (mmm) REVERT: a 374 HIS cc_start: 0.8133 (t-90) cc_final: 0.7756 (t-90) REVERT: a 410 MET cc_start: 0.8007 (ttm) cc_final: 0.7616 (ttm) REVERT: a 413 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8194 (tm-30) REVERT: B 116 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7107 (mmmt) REVERT: B 130 ASP cc_start: 0.8533 (t0) cc_final: 0.8275 (t0) REVERT: b 311 ASP cc_start: 0.8926 (m-30) cc_final: 0.8597 (t0) REVERT: b 374 HIS cc_start: 0.8034 (t-90) cc_final: 0.7705 (t-90) REVERT: b 418 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8730 (tm-30) outliers start: 16 outliers final: 16 residues processed: 190 average time/residue: 0.0947 time to fit residues: 24.4488 Evaluate side-chains 185 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 419 TYR Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.096758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076874 restraints weight = 27495.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.079424 restraints weight = 17082.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.081250 restraints weight = 12741.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.082474 restraints weight = 10487.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.083332 restraints weight = 9169.863| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 10104 Z= 0.215 Angle : 1.082 59.200 13839 Z= 0.563 Chirality : 0.047 0.377 1743 Planarity : 0.004 0.046 1593 Dihedral : 7.727 53.214 2934 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.10 % Favored : 91.81 % Rotamer: Outliers : 1.97 % Allowed : 19.46 % Favored : 78.57 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.26), residues: 1074 helix: 0.99 (0.27), residues: 387 sheet: 0.02 (0.55), residues: 102 loop : -0.62 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 248 TYR 0.029 0.001 TYR B 62 PHE 0.008 0.001 PHE B 233 TRP 0.022 0.002 TRP C 210 HIS 0.005 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9996) covalent geometry : angle 1.01750 (13536) SS BOND : bond 0.00513 ( 21) SS BOND : angle 3.05732 ( 42) hydrogen bonds : bond 0.03864 ( 402) hydrogen bonds : angle 4.11412 ( 1044) link_ALPHA1-3 : bond 0.01020 ( 3) link_ALPHA1-3 : angle 1.16948 ( 9) link_ALPHA1-6 : bond 0.00618 ( 9) link_ALPHA1-6 : angle 1.44282 ( 27) link_BETA1-4 : bond 0.00689 ( 39) link_BETA1-4 : angle 2.89828 ( 117) link_BETA1-6 : bond 0.00204 ( 3) link_BETA1-6 : angle 1.44775 ( 9) link_NAG-ASN : bond 0.00322 ( 33) link_NAG-ASN : angle 2.72325 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1476.96 seconds wall clock time: 26 minutes 32.06 seconds (1592.06 seconds total)