Starting phenix.real_space_refine on Fri Jul 3 17:33:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ejh_28182/07_2026/8ejh_28182.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejh_28182/07_2026/8ejh_28182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ejh_28182/07_2026/8ejh_28182.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ejh_28182/07_2026/8ejh_28182.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ejh_28182/07_2026/8ejh_28182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejh_28182/07_2026/8ejh_28182.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejh_28182/07_2026/8ejh_28182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejh_28182/07_2026/8ejh_28182.cif" } resolution = 3.71 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= 0.033 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 105 5.16 5 C 9492 2.51 5 N 2418 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15186 Number of models: 1 Model: "" Number of chains: 45 Chain: "C" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1522 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1522 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 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: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1522 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 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: "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: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "h" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "l" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} 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 chiralities: 3 Chain: "E" 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 chiralities: 5 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 chiralities: 2 Chain: "G" 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 chiralities: 3 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 chiralities: 2 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 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 chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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 chiralities: 5 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 chiralities: 2 Chain: "R" 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 chiralities: 3 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 chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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 chiralities: 5 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 chiralities: 2 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 chiralities: 3 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 chiralities: 2 Chain: "f" 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 chiralities: 3 Chain: "g" 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 chiralities: 3 Chain: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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 chiralities: 2 Chain: "k" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 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 chiralities: 2 Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.59, per 1000 atoms: 0.24 Number of scatterers: 15186 At special positions: 0 Unit cell: (135.7, 148.35, 121.9, 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 105 16.00 O 3171 8.00 N 2418 7.00 C 9492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.04 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.02 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.08 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.06 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 104 " distance=2.08 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 104 " distance=2.06 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 104 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN V 4 " - " MAN V 5 " " MAN i 4 " - " MAN i 5 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA E 3 " - " MAN J 201 " " MAN E 4 " - " MAN E 5 " " BMA P 3 " - " MAN h 201 " " MAN P 4 " - " MAN P 5 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " " BMA Y 3 " - " MAN H 201 " " MAN Y 4 " - " MAN Y 5 " " BMA i 3 " - " MAN i 4 " " MAN i 6 " - " MAN i 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 6 " " BMA Y 3 " - " MAN Y 4 " " BMA i 3 " - " MAN i 6 " " BMA k 3 " - " MAN k 6 " 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 G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " 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 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG m 1 " - " NAG m 2 " 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 I 1 " - " ASN C 119 " " NAG M 1 " - " ASN C 167 " " NAG N 1 " - " ASN C 224 " " NAG O 1 " - " ASN B 79 " " NAG P 1 " - " ASN B 89 " " NAG Q 1 " - " ASN B 99 " " NAG R 1 " - " ASN B 109 " " NAG S 1 " - " ASN B 119 " " NAG T 1 " - " ASN B 167 " " NAG U 1 " - " ASN B 224 " " NAG V 1 " - " ASN c 365 " " NAG W 1 " - " ASN c 373 " " NAG X 1 " - " ASN A 79 " " NAG Y 1 " - " ASN A 89 " " NAG Z 1 " - " ASN A 99 " " 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 A 109 " " NAG e 1 " - " ASN A 119 " " NAG f 1 " - " ASN A 167 " " NAG g 1 " - " ASN A 224 " " NAG i 1 " - " ASN b 365 " " NAG j 1 " - " ASN b 373 " " NAG k 1 " - " ASN a 365 " " NAG m 1 " - " ASN a 373 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 737.0 milliseconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3270 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 30 sheets defined 26.9% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 76 through 81 removed outlier: 4.292A pdb=" N MET C 80 " --> pdb=" O THR C 77 " (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 183 through 195 Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.293A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (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 183 through 195 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'c' and resid 294 through 301 removed outlier: 4.146A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) Processing helix chain 'c' and resid 302 through 304 No H-bonds generated for 'chain 'c' and resid 302 through 304' Processing helix chain 'c' and resid 308 through 326 removed outlier: 3.707A pdb=" N LEU c 326 " --> pdb=" O ALA c 322 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 339 Processing helix chain 'c' and resid 340 through 345 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.969A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 424 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 76 through 81 removed outlier: 4.292A pdb=" N MET A 80 " --> pdb=" O THR A 77 " (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 183 through 195 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'b' and resid 294 through 301 removed outlier: 4.146A pdb=" N CYS b 301 " --> pdb=" O ALA b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 302 through 304 No H-bonds generated for 'chain 'b' and resid 302 through 304' Processing helix chain 'b' and resid 308 through 326 removed outlier: 3.707A pdb=" N LEU b 326 " --> pdb=" O ALA b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 339 Processing helix chain 'b' and resid 340 through 345 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.969A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 424 Processing helix chain 'a' and resid 294 through 301 removed outlier: 4.146A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) Processing helix chain 'a' and resid 302 through 304 No H-bonds generated for 'chain 'a' and resid 302 through 304' Processing helix chain 'a' and resid 308 through 326 removed outlier: 3.707A pdb=" N LEU a 326 " --> pdb=" O ALA a 322 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 339 Processing helix chain 'a' and resid 340 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.969A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 424 Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.920A pdb=" N PHE H 37 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'J' and resid 29 through 37 removed outlier: 3.920A pdb=" N PHE J 37 " --> pdb=" O PHE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 72 Processing helix chain 'J' and resid 82 through 84 No H-bonds generated for 'chain 'J' and resid 82 through 84' Processing helix chain 'K' and resid 95 through 99 Processing helix chain 'h' and resid 29 through 37 removed outlier: 3.920A pdb=" N PHE h 37 " --> pdb=" O PHE h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 69 through 72 Processing helix chain 'h' and resid 82 through 84 No H-bonds generated for 'chain 'h' and resid 82 through 84' Processing helix chain 'l' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 72 Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 88 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 88 Processing sheet with id=AA5, first strand: chain 'c' and resid 279 through 280 Processing sheet with id=AA6, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AA7, first strand: chain 'A' and resid 66 through 72 Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 88 Processing sheet with id=AA9, first strand: chain 'b' and resid 279 through 280 Processing sheet with id=AB1, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'a' and resid 279 through 280 Processing sheet with id=AB3, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.528A pdb=" N SER H 79 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS H 104 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP H 118 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG H 106 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.022A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'J' and resid 7 through 9 removed outlier: 3.528A pdb=" N SER J 79 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG J 43 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS J 104 " --> pdb=" O TRP J 118 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP J 118 " --> pdb=" O CYS J 104 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG J 106 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG J 43 " --> pdb=" O TRP J 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.022A pdb=" N GLN K 43 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU K 52 " --> pdb=" O GLN K 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AC7, first strand: chain 'h' and resid 7 through 9 removed outlier: 3.528A pdb=" N SER h 79 " --> pdb=" O SER h 88 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP h 52 " --> pdb=" O ARG h 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG h 43 " --> pdb=" O TRP h 52 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS h 104 " --> pdb=" O TRP h 118 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP h 118 " --> pdb=" O CYS h 104 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG h 106 " --> pdb=" O ASP h 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP h 52 " --> pdb=" O ARG h 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG h 43 " --> pdb=" O TRP h 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'l' and resid 4 through 5 Processing sheet with id=AD2, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.022A pdb=" N GLN l 43 " --> pdb=" O LEU l 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU l 52 " --> pdb=" O GLN l 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 10 through 12 606 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2736 1.32 - 1.46: 5318 1.46 - 1.59: 7267 1.59 - 1.73: 42 1.73 - 1.87: 153 Bond restraints: 15516 Sorted by residual: bond pdb=" CB HIS K 44 " pdb=" CG HIS K 44 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.41e+01 bond pdb=" CB HIS L 44 " pdb=" CG HIS L 44 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.40e+01 bond pdb=" CB HIS l 44 " pdb=" CG HIS l 44 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.39e+01 bond pdb=" CB HIS L 106 " pdb=" CG HIS L 106 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.06e+01 bond pdb=" CB HIS l 106 " pdb=" CG HIS l 106 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.03e+01 ... (remaining 15511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16497 2.01 - 4.02: 3590 4.02 - 6.02: 778 6.02 - 8.03: 126 8.03 - 10.04: 48 Bond angle restraints: 21039 Sorted by residual: angle pdb=" N ASP c 311 " pdb=" CA ASP c 311 " pdb=" C ASP c 311 " ideal model delta sigma weight residual 111.69 101.98 9.71 1.23e+00 6.61e-01 6.24e+01 angle pdb=" N ASP a 311 " pdb=" CA ASP a 311 " pdb=" C ASP a 311 " ideal model delta sigma weight residual 111.69 102.01 9.68 1.23e+00 6.61e-01 6.20e+01 angle pdb=" N ASP b 311 " pdb=" CA ASP b 311 " pdb=" C ASP b 311 " ideal model delta sigma weight residual 111.69 102.01 9.68 1.23e+00 6.61e-01 6.19e+01 angle pdb=" C GLN h 44 " pdb=" N PRO h 45 " pdb=" CA PRO h 45 " ideal model delta sigma weight residual 119.66 124.99 -5.33 7.30e-01 1.88e+00 5.32e+01 angle pdb=" C GLN J 44 " pdb=" N PRO J 45 " pdb=" CA PRO J 45 " ideal model delta sigma weight residual 119.66 124.98 -5.32 7.30e-01 1.88e+00 5.30e+01 ... (remaining 21034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 8100 16.35 - 32.69: 240 32.69 - 49.04: 57 49.04 - 65.38: 48 65.38 - 81.73: 12 Dihedral angle restraints: 8457 sinusoidal: 3351 harmonic: 5106 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 104 " pdb=" CB CYS K 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.20 -62.20 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS l 23 " pdb=" SG CYS l 23 " pdb=" SG CYS l 104 " pdb=" CB CYS l 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.20 -62.20 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.19 -62.19 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 8454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1641 0.101 - 0.202: 564 0.202 - 0.302: 236 0.302 - 0.403: 103 0.403 - 0.504: 60 Chirality restraints: 2604 Sorted by residual: chirality pdb=" C1 MAN V 6 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 6 " pdb=" O5 MAN V 6 " both_signs ideal model delta sigma weight residual False 2.40 2.13 0.27 2.00e-02 2.50e+03 1.89e+02 chirality pdb=" C1 MAN i 6 " pdb=" O6 BMA i 3 " pdb=" C2 MAN i 6 " pdb=" O5 MAN i 6 " both_signs ideal model delta sigma weight residual False 2.40 2.13 0.27 2.00e-02 2.50e+03 1.87e+02 chirality pdb=" C1 MAN k 6 " pdb=" O6 BMA k 3 " pdb=" C2 MAN k 6 " pdb=" O5 MAN k 6 " both_signs ideal model delta sigma weight residual False 2.40 2.13 0.27 2.00e-02 2.50e+03 1.86e+02 ... (remaining 2601 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.238 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" C7 NAG Y 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " -0.238 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" C7 NAG P 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.238 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" C7 NAG E 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.030 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4647 2.84 - 3.35: 13654 3.35 - 3.87: 25437 3.87 - 4.38: 29641 4.38 - 4.90: 47957 Nonbonded interactions: 121336 Sorted by model distance: nonbonded pdb=" O4 MAN P 4 " pdb=" O6 MAN P 4 " model vdw 2.321 3.040 nonbonded pdb=" O4 MAN E 4 " pdb=" O6 MAN E 4 " model vdw 2.321 3.040 nonbonded pdb=" O4 MAN Y 4 " pdb=" O6 MAN Y 4 " model vdw 2.321 3.040 nonbonded pdb=" O4 MAN k 4 " pdb=" O6 MAN k 4 " model vdw 2.380 3.040 nonbonded pdb=" O4 MAN i 4 " pdb=" O6 MAN i 4 " model vdw 2.380 3.040 ... (remaining 121331 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'd' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'Q' selection = chain 'S' selection = chain 'W' selection = chain 'Z' selection = chain 'e' selection = chain 'j' selection = chain 'm' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'h' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'V' selection = chain 'i' selection = chain 'k' } 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.850 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 0.117 15642 Z= 1.158 Angle : 1.906 13.568 21390 Z= 1.167 Chirality : 0.146 0.504 2604 Planarity : 0.011 0.193 2514 Dihedral : 10.158 81.728 5106 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.18 (0.20), residues: 1731 helix: -0.37 (0.25), residues: 372 sheet: 0.26 (0.26), residues: 375 loop : -0.05 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG h 75 TYR 0.048 0.007 TYR B 253 PHE 0.027 0.006 PHE l 99 TRP 0.075 0.010 TRP H 52 HIS 0.006 0.002 HIS H 113 Details of bonding type rmsd/Z covalent geometry : bond 0.02127 / 1.13 (15516) covalent geometry : angle 1.82534 / 1.16 (21039) SS BOND : bond 0.02120 / 1.46 ( 27) SS BOND : angle 3.70606 / 2.30 ( 54) hydrogen bonds : bond 0.18297 / 12.17 ( 552) hydrogen bonds : angle 7.48017 / 5.31 ( 1566) link_ALPHA1-2 : bond 0.08703 / 4.02 ( 3) link_ALPHA1-2 : angle 5.58010 / 3.21 ( 9) link_ALPHA1-3 : bond 0.07270 / 3.60 ( 12) link_ALPHA1-3 : angle 6.47357 / 3.77 ( 36) link_ALPHA1-6 : bond 0.04013 / 2.01 ( 6) link_ALPHA1-6 : angle 2.04702 / 1.19 ( 18) link_BETA1-4 : bond 0.07223 / 4.36 ( 45) link_BETA1-4 : angle 5.48432 / 3.45 ( 135) link_NAG-ASN : bond 0.07388 / 4.45 ( 33) link_NAG-ASN : angle 3.11118 / 1.99 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 0.690 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: C 80 MET cc_start: 0.8364 (mmm) cc_final: 0.7641 (mmm) REVERT: C 194 MET cc_start: 0.8339 (tpp) cc_final: 0.7888 (tpp) REVERT: B 80 MET cc_start: 0.8297 (mmm) cc_final: 0.7500 (mmt) REVERT: B 194 MET cc_start: 0.8366 (tpp) cc_final: 0.8139 (tpp) REVERT: A 80 MET cc_start: 0.8351 (mmm) cc_final: 0.7756 (mmt) REVERT: A 194 MET cc_start: 0.8278 (tpp) cc_final: 0.7907 (ttm) REVERT: H 13 LEU cc_start: 0.8014 (mt) cc_final: 0.7703 (pp) REVERT: H 52 TRP cc_start: 0.8554 (t60) cc_final: 0.8283 (t60) REVERT: H 56 ILE cc_start: 0.9329 (tt) cc_final: 0.9052 (tt) REVERT: H 68 ASN cc_start: 0.8838 (t0) cc_final: 0.8399 (t0) REVERT: H 80 VAL cc_start: 0.8784 (p) cc_final: 0.8571 (t) REVERT: H 98 ASP cc_start: 0.8127 (m-30) cc_final: 0.7785 (m-30) REVERT: L 3 THR cc_start: 0.9317 (p) cc_final: 0.8990 (p) REVERT: L 5 THR cc_start: 0.8172 (m) cc_final: 0.7895 (p) REVERT: L 18 ARG cc_start: 0.8162 (ttm170) cc_final: 0.7704 (ttp80) REVERT: L 90 THR cc_start: 0.8425 (m) cc_final: 0.8115 (p) REVERT: L 99 PHE cc_start: 0.6940 (m-80) cc_final: 0.6723 (m-80) REVERT: J 52 TRP cc_start: 0.8638 (t60) cc_final: 0.8388 (t60) REVERT: J 87 PHE cc_start: 0.8165 (p90) cc_final: 0.7903 (p90) REVERT: J 98 ASP cc_start: 0.7786 (m-30) cc_final: 0.7563 (m-30) REVERT: J 122 THR cc_start: 0.7888 (m) cc_final: 0.7672 (p) REVERT: K 5 THR cc_start: 0.8308 (m) cc_final: 0.8083 (p) REVERT: K 90 THR cc_start: 0.8444 (m) cc_final: 0.8235 (p) REVERT: K 99 PHE cc_start: 0.6802 (m-80) cc_final: 0.6418 (m-80) REVERT: h 13 LEU cc_start: 0.7856 (mt) cc_final: 0.7512 (pp) REVERT: h 87 PHE cc_start: 0.8310 (p90) cc_final: 0.8095 (p90) REVERT: l 18 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7699 (ttp80) REVERT: l 90 THR cc_start: 0.8466 (m) cc_final: 0.8188 (p) REVERT: l 99 PHE cc_start: 0.6714 (m-80) cc_final: 0.6325 (m-80) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.1479 time to fit residues: 112.3959 Evaluate side-chains 283 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 302 ASN b 302 ASN a 302 ASN a 416 GLN L 105 GLN L 106 HIS J 68 ASN K 6 GLN K 105 GLN l 6 GLN l 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.109304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084587 restraints weight = 36943.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088184 restraints weight = 19728.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.090588 restraints weight = 13659.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.092181 restraints weight = 10856.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.093259 restraints weight = 9354.477| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15642 Z= 0.197 Angle : 0.895 10.656 21390 Z= 0.432 Chirality : 0.047 0.286 2604 Planarity : 0.005 0.043 2514 Dihedral : 5.564 22.977 1902 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.75 % Allowed : 10.27 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.07 (0.20), residues: 1731 helix: 0.43 (0.28), residues: 378 sheet: 0.30 (0.25), residues: 405 loop : -0.32 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 325 TYR 0.024 0.002 TYR J 112C PHE 0.022 0.002 PHE H 30 TRP 0.039 0.002 TRP h 52 HIS 0.009 0.002 HIS a 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (15516) covalent geometry : angle 0.81690 / 0.42 (21039) SS BOND : bond 0.00589 / 0.37 ( 27) SS BOND : angle 1.42011 / 0.88 ( 54) hydrogen bonds : bond 0.05427 / 3.71 ( 552) hydrogen bonds : angle 5.62560 / 3.93 ( 1566) link_ALPHA1-2 : bond 0.00778 / 0.36 ( 3) link_ALPHA1-2 : angle 2.11980 / 1.23 ( 9) link_ALPHA1-3 : bond 0.01908 / 0.93 ( 12) link_ALPHA1-3 : angle 4.20035 / 2.57 ( 36) link_ALPHA1-6 : bond 0.01098 / 0.60 ( 6) link_ALPHA1-6 : angle 1.38318 / 0.76 ( 18) link_BETA1-4 : bond 0.01168 / 0.74 ( 45) link_BETA1-4 : angle 3.53718 / 2.25 ( 135) link_NAG-ASN : bond 0.00658 / 0.40 ( 33) link_NAG-ASN : angle 2.45668 / 1.52 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 359 time to evaluate : 0.575 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: C 96 MET cc_start: 0.7732 (mmm) cc_final: 0.7427 (mmm) REVERT: C 153 MET cc_start: 0.8745 (ttt) cc_final: 0.8334 (ttt) REVERT: C 161 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8031 (tptt) REVERT: B 116 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8580 (mmmt) REVERT: B 156 ASP cc_start: 0.7664 (t70) cc_final: 0.7412 (t0) REVERT: B 161 LYS cc_start: 0.8455 (ttmt) cc_final: 0.7688 (tptt) REVERT: c 282 ARG cc_start: 0.8443 (tpt90) cc_final: 0.7911 (tpm170) REVERT: c 303 GLU cc_start: 0.6142 (tp30) cc_final: 0.5507 (tp30) REVERT: c 351 MET cc_start: 0.8854 (tpp) cc_final: 0.8594 (tpp) REVERT: c 420 MET cc_start: 0.7238 (mmt) cc_final: 0.6175 (tpt) REVERT: A 96 MET cc_start: 0.7753 (mmm) cc_final: 0.7384 (mmm) REVERT: A 116 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8414 (mmmt) REVERT: A 134 MET cc_start: 0.9425 (tpp) cc_final: 0.9099 (tpp) REVERT: A 156 ASP cc_start: 0.8031 (p0) cc_final: 0.7735 (p0) REVERT: A 161 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8015 (tptt) REVERT: b 284 MET cc_start: 0.8219 (mtm) cc_final: 0.7626 (mtm) REVERT: b 303 GLU cc_start: 0.6211 (tp30) cc_final: 0.5757 (tp30) REVERT: b 305 HIS cc_start: 0.7371 (m90) cc_final: 0.6941 (m-70) REVERT: b 332 MET cc_start: 0.7479 (mmp) cc_final: 0.7245 (mmm) REVERT: b 420 MET cc_start: 0.7330 (mmt) cc_final: 0.6883 (tpt) REVERT: b 423 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7831 (mp10) REVERT: a 284 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7947 (mtp) REVERT: a 306 ASP cc_start: 0.8414 (p0) cc_final: 0.8148 (p0) REVERT: a 326 LEU cc_start: 0.7966 (mt) cc_final: 0.7270 (mt) REVERT: a 359 MET cc_start: 0.9024 (mtt) cc_final: 0.8777 (mtm) REVERT: a 409 ASN cc_start: 0.8821 (m-40) cc_final: 0.8403 (m110) REVERT: a 420 MET cc_start: 0.7453 (mmt) cc_final: 0.6924 (tpt) REVERT: H 6 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6327 (mm-30) REVERT: H 13 LEU cc_start: 0.7342 (mt) cc_final: 0.7093 (pp) REVERT: H 51 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7010 (tt0) REVERT: H 53 ILE cc_start: 0.8134 (mt) cc_final: 0.7804 (mt) REVERT: H 78 ILE cc_start: 0.8449 (mt) cc_final: 0.8169 (tp) REVERT: H 98 ASP cc_start: 0.7333 (m-30) cc_final: 0.6917 (m-30) REVERT: H 112 TYR cc_start: 0.7889 (p90) cc_final: 0.7089 (p90) REVERT: L 17 GLU cc_start: 0.6849 (mp0) cc_final: 0.6571 (mp0) REVERT: L 18 ARG cc_start: 0.8362 (ttm170) cc_final: 0.7803 (ttp80) REVERT: L 90 THR cc_start: 0.8210 (m) cc_final: 0.7817 (p) REVERT: L 94 LEU cc_start: 0.7707 (tp) cc_final: 0.7024 (tt) REVERT: L 99 PHE cc_start: 0.6827 (m-80) cc_final: 0.5854 (m-80) REVERT: L 125 GLU cc_start: 0.6715 (tt0) cc_final: 0.6359 (tt0) REVERT: J 5 GLN cc_start: 0.7039 (tp40) cc_final: 0.6590 (tp-100) REVERT: J 43 ARG cc_start: 0.8100 (ttp-170) cc_final: 0.7811 (ttp-170) REVERT: J 52 TRP cc_start: 0.7677 (t60) cc_final: 0.7411 (t60) REVERT: J 87 PHE cc_start: 0.8495 (p90) cc_final: 0.8286 (p90) REVERT: J 98 ASP cc_start: 0.7042 (m-30) cc_final: 0.6614 (m-30) REVERT: K 5 THR cc_start: 0.7931 (m) cc_final: 0.7717 (p) REVERT: K 18 ARG cc_start: 0.8416 (ttm170) cc_final: 0.7754 (ttp80) REVERT: K 90 THR cc_start: 0.8128 (m) cc_final: 0.7836 (p) REVERT: K 94 LEU cc_start: 0.7882 (tp) cc_final: 0.7478 (tt) REVERT: K 99 PHE cc_start: 0.7025 (m-80) cc_final: 0.6723 (m-80) REVERT: h 43 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7994 (mtm110) REVERT: h 53 ILE cc_start: 0.8156 (mt) cc_final: 0.7592 (mt) REVERT: h 78 ILE cc_start: 0.8373 (mt) cc_final: 0.7813 (tp) REVERT: h 87 PHE cc_start: 0.8497 (p90) cc_final: 0.8040 (p90) REVERT: h 112 TYR cc_start: 0.8155 (p90) cc_final: 0.7811 (p90) REVERT: l 17 GLU cc_start: 0.7504 (mp0) cc_final: 0.7079 (mp0) REVERT: l 18 ARG cc_start: 0.8606 (ttm170) cc_final: 0.7768 (ttp80) REVERT: l 90 THR cc_start: 0.8191 (m) cc_final: 0.7789 (p) REVERT: l 98 ASP cc_start: 0.8364 (m-30) cc_final: 0.8095 (m-30) REVERT: l 99 PHE cc_start: 0.7009 (m-80) cc_final: 0.6184 (m-80) REVERT: l 125 GLU cc_start: 0.6048 (tt0) cc_final: 0.5767 (tt0) outliers start: 27 outliers final: 17 residues processed: 371 average time/residue: 0.1351 time to fit residues: 72.7891 Evaluate side-chains 308 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 290 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 68 optimal weight: 0.0470 chunk 141 optimal weight: 0.1980 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 151 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 HIS C 170 HIS B 170 HIS A 92 HIS A 170 HIS L 106 HIS l 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.108839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085443 restraints weight = 36570.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089011 restraints weight = 18805.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.091437 restraints weight = 12751.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.093044 restraints weight = 9976.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.094048 restraints weight = 8487.729| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15642 Z= 0.153 Angle : 0.795 11.586 21390 Z= 0.378 Chirality : 0.043 0.256 2604 Planarity : 0.004 0.039 2514 Dihedral : 5.456 25.030 1902 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.86 % Allowed : 11.57 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.14 (0.20), residues: 1731 helix: 0.63 (0.28), residues: 375 sheet: 0.32 (0.25), residues: 420 loop : -0.53 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 67 TYR 0.027 0.002 TYR J 112C PHE 0.016 0.002 PHE H 30 TRP 0.025 0.002 TRP B 210 HIS 0.006 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (15516) covalent geometry : angle 0.72285 / 0.36 (21039) SS BOND : bond 0.00465 / 0.30 ( 27) SS BOND : angle 2.03076 / 1.15 ( 54) hydrogen bonds : bond 0.04636 / 3.18 ( 552) hydrogen bonds : angle 5.38786 / 3.78 ( 1566) link_ALPHA1-2 : bond 0.00342 / 0.16 ( 3) link_ALPHA1-2 : angle 1.73484 / 0.99 ( 9) link_ALPHA1-3 : bond 0.01708 / 0.82 ( 12) link_ALPHA1-3 : angle 3.93042 / 2.38 ( 36) link_ALPHA1-6 : bond 0.00948 / 0.52 ( 6) link_ALPHA1-6 : angle 1.25456 / 0.70 ( 18) link_BETA1-4 : bond 0.01001 / 0.63 ( 45) link_BETA1-4 : angle 3.02419 / 1.92 ( 135) link_NAG-ASN : bond 0.00501 / 0.31 ( 33) link_NAG-ASN : angle 2.18330 / 1.34 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 315 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8395 (mtm) cc_final: 0.8180 (mtm) REVERT: C 153 MET cc_start: 0.8722 (ttt) cc_final: 0.8325 (ttt) REVERT: C 156 ASP cc_start: 0.7384 (t70) cc_final: 0.6406 (t0) REVERT: C 161 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8195 (ttpp) REVERT: C 194 MET cc_start: 0.8874 (tpp) cc_final: 0.8605 (tpp) REVERT: B 116 LYS cc_start: 0.8944 (mmtm) cc_final: 0.8667 (mmmt) REVERT: B 156 ASP cc_start: 0.7757 (t70) cc_final: 0.7534 (t0) REVERT: B 161 LYS cc_start: 0.8452 (ttmt) cc_final: 0.7726 (tptt) REVERT: c 282 ARG cc_start: 0.8468 (tpt90) cc_final: 0.7917 (tpm170) REVERT: c 303 GLU cc_start: 0.6026 (tp30) cc_final: 0.5413 (tp30) REVERT: c 326 LEU cc_start: 0.7917 (mp) cc_final: 0.7338 (tp) REVERT: c 420 MET cc_start: 0.7246 (mmt) cc_final: 0.6265 (tpt) REVERT: A 116 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8482 (mmmt) REVERT: A 156 ASP cc_start: 0.8067 (p0) cc_final: 0.7736 (p0) REVERT: A 161 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8006 (tptt) REVERT: A 194 MET cc_start: 0.8899 (tpp) cc_final: 0.8655 (tpp) REVERT: b 284 MET cc_start: 0.8152 (mtm) cc_final: 0.7702 (mtm) REVERT: b 305 HIS cc_start: 0.7376 (m90) cc_final: 0.7056 (m170) REVERT: b 332 MET cc_start: 0.7457 (mmp) cc_final: 0.7218 (mmm) REVERT: b 418 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8453 (mt-10) REVERT: b 420 MET cc_start: 0.7653 (mmt) cc_final: 0.7067 (tpt) REVERT: a 282 ARG cc_start: 0.8344 (tpt90) cc_final: 0.8008 (tpm170) REVERT: a 284 MET cc_start: 0.8441 (mtp) cc_final: 0.8015 (mtp) REVERT: a 306 ASP cc_start: 0.8398 (p0) cc_final: 0.8138 (p0) REVERT: a 326 LEU cc_start: 0.7770 (mt) cc_final: 0.7144 (mt) REVERT: a 420 MET cc_start: 0.8024 (mmt) cc_final: 0.7314 (tpt) REVERT: H 13 LEU cc_start: 0.7409 (mt) cc_final: 0.7151 (pp) REVERT: H 51 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7040 (tt0) REVERT: H 53 ILE cc_start: 0.8199 (mt) cc_final: 0.7668 (mt) REVERT: H 98 ASP cc_start: 0.7353 (m-30) cc_final: 0.6916 (m-30) REVERT: H 110 TYR cc_start: 0.8160 (t80) cc_final: 0.7836 (t80) REVERT: H 112 TYR cc_start: 0.7998 (p90) cc_final: 0.7129 (p90) REVERT: L 17 GLU cc_start: 0.7087 (mp0) cc_final: 0.6785 (mp0) REVERT: L 18 ARG cc_start: 0.8409 (ttm170) cc_final: 0.7813 (ttp80) REVERT: L 90 THR cc_start: 0.8246 (m) cc_final: 0.7915 (p) REVERT: L 94 LEU cc_start: 0.7737 (tp) cc_final: 0.7067 (tt) REVERT: L 99 PHE cc_start: 0.7195 (m-80) cc_final: 0.6243 (m-80) REVERT: L 122 THR cc_start: 0.7802 (p) cc_final: 0.7599 (p) REVERT: L 125 GLU cc_start: 0.5894 (tt0) cc_final: 0.5692 (tt0) REVERT: J 5 GLN cc_start: 0.7147 (tp40) cc_final: 0.6676 (tp-100) REVERT: J 43 ARG cc_start: 0.8101 (ttp-170) cc_final: 0.7789 (ttp-170) REVERT: J 52 TRP cc_start: 0.7842 (t60) cc_final: 0.7258 (t60) REVERT: J 87 PHE cc_start: 0.8377 (p90) cc_final: 0.8144 (p90) REVERT: J 98 ASP cc_start: 0.7162 (m-30) cc_final: 0.6642 (m-30) REVERT: K 5 THR cc_start: 0.7922 (m) cc_final: 0.7707 (p) REVERT: K 17 GLU cc_start: 0.7410 (mp0) cc_final: 0.7032 (mp0) REVERT: K 90 THR cc_start: 0.8150 (m) cc_final: 0.7845 (p) REVERT: K 94 LEU cc_start: 0.7692 (tp) cc_final: 0.7384 (tt) REVERT: K 99 PHE cc_start: 0.7274 (m-80) cc_final: 0.6639 (m-80) REVERT: K 122 THR cc_start: 0.8397 (p) cc_final: 0.8137 (p) REVERT: h 53 ILE cc_start: 0.8104 (mt) cc_final: 0.7591 (mt) REVERT: h 112 TYR cc_start: 0.8017 (p90) cc_final: 0.7363 (p90) REVERT: l 17 GLU cc_start: 0.7596 (mp0) cc_final: 0.7177 (mp0) REVERT: l 18 ARG cc_start: 0.8311 (ttm170) cc_final: 0.7898 (ttp80) REVERT: l 90 THR cc_start: 0.8217 (m) cc_final: 0.7827 (p) REVERT: l 94 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7622 (tt) REVERT: l 99 PHE cc_start: 0.7148 (m-80) cc_final: 0.6486 (m-80) REVERT: l 125 GLU cc_start: 0.6327 (tt0) cc_final: 0.5899 (tt0) outliers start: 44 outliers final: 25 residues processed: 337 average time/residue: 0.1214 time to fit residues: 60.2682 Evaluate side-chains 310 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 292 CYS Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain l residue 1 GLU Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 158 ASN c 423 GLN L 106 HIS K 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.101796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078278 restraints weight = 37393.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081498 restraints weight = 19576.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083640 restraints weight = 13591.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.084970 restraints weight = 10871.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085969 restraints weight = 9479.419| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 15642 Z= 0.299 Angle : 0.907 10.723 21390 Z= 0.426 Chirality : 0.047 0.234 2604 Planarity : 0.005 0.043 2514 Dihedral : 5.637 24.571 1902 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.83 % Allowed : 12.80 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.44 (0.20), residues: 1731 helix: 0.66 (0.28), residues: 375 sheet: 0.05 (0.25), residues: 402 loop : -0.81 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 115 TYR 0.030 0.002 TYR b 419 PHE 0.015 0.003 PHE B 157 TRP 0.049 0.003 TRP H 52 HIS 0.007 0.002 HIS L 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.30 (15516) covalent geometry : angle 0.84896 / 0.41 (21039) SS BOND : bond 0.00873 / 0.54 ( 27) SS BOND : angle 2.15801 / 1.20 ( 54) hydrogen bonds : bond 0.04919 / 3.34 ( 552) hydrogen bonds : angle 5.50454 / 3.86 ( 1566) link_ALPHA1-2 : bond 0.00059 / 0.03 ( 3) link_ALPHA1-2 : angle 1.73386 / 0.98 ( 9) link_ALPHA1-3 : bond 0.01836 / 0.79 ( 12) link_ALPHA1-3 : angle 4.03037 / 2.47 ( 36) link_ALPHA1-6 : bond 0.00623 / 0.35 ( 6) link_ALPHA1-6 : angle 1.66545 / 0.98 ( 18) link_BETA1-4 : bond 0.00718 / 0.46 ( 45) link_BETA1-4 : angle 2.74959 / 1.74 ( 135) link_NAG-ASN : bond 0.00431 / 0.27 ( 33) link_NAG-ASN : angle 2.22504 / 1.38 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7612 (pm20) cc_final: 0.7348 (pm20) REVERT: C 156 ASP cc_start: 0.7924 (t70) cc_final: 0.7224 (t0) REVERT: C 161 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8354 (ttpp) REVERT: C 194 MET cc_start: 0.8947 (tpp) cc_final: 0.8419 (tpp) REVERT: C 214 MET cc_start: 0.8010 (ptp) cc_final: 0.7712 (ptp) REVERT: B 69 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7629 (mt0) REVERT: B 116 LYS cc_start: 0.9161 (mmtm) cc_final: 0.8866 (mmmt) REVERT: B 156 ASP cc_start: 0.8110 (t70) cc_final: 0.7099 (t0) REVERT: B 161 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8223 (ttpp) REVERT: c 282 ARG cc_start: 0.8550 (tpt90) cc_final: 0.7991 (tpm170) REVERT: c 311 ASP cc_start: 0.8364 (t0) cc_final: 0.8083 (t0) REVERT: c 415 LEU cc_start: 0.8628 (mt) cc_final: 0.8416 (pp) REVERT: c 420 MET cc_start: 0.7320 (mmt) cc_final: 0.6395 (tpt) REVERT: A 80 MET cc_start: 0.8905 (mmt) cc_final: 0.8117 (mpp) REVERT: A 104 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: A 116 LYS cc_start: 0.9146 (mmtm) cc_final: 0.8883 (mmmt) REVERT: A 156 ASP cc_start: 0.7954 (p0) cc_final: 0.7666 (p0) REVERT: A 161 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8227 (ttpp) REVERT: b 284 MET cc_start: 0.8245 (mtm) cc_final: 0.7740 (mtm) REVERT: b 311 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8273 (t0) REVERT: b 332 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6778 (tpp) REVERT: b 419 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6427 (t80) REVERT: b 420 MET cc_start: 0.7610 (mmt) cc_final: 0.6694 (tpt) REVERT: a 284 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7974 (mtp) REVERT: a 311 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7417 (t0) REVERT: a 345 ILE cc_start: 0.9088 (mm) cc_final: 0.8862 (mm) REVERT: a 348 GLN cc_start: 0.5351 (mt0) cc_final: 0.4467 (tt0) REVERT: a 420 MET cc_start: 0.7923 (mmt) cc_final: 0.7295 (tpt) REVERT: H 6 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6137 (mm-30) REVERT: H 13 LEU cc_start: 0.7551 (mt) cc_final: 0.7241 (pp) REVERT: H 51 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7087 (tt0) REVERT: H 98 ASP cc_start: 0.7641 (m-30) cc_final: 0.7297 (m-30) REVERT: L 17 GLU cc_start: 0.7398 (mp0) cc_final: 0.7072 (mp0) REVERT: L 18 ARG cc_start: 0.8457 (ttm170) cc_final: 0.7560 (ttp80) REVERT: L 90 THR cc_start: 0.8628 (m) cc_final: 0.8320 (p) REVERT: L 94 LEU cc_start: 0.7840 (tp) cc_final: 0.7234 (tt) REVERT: L 99 PHE cc_start: 0.7461 (m-80) cc_final: 0.6641 (m-80) REVERT: J 5 GLN cc_start: 0.7278 (tp40) cc_final: 0.6925 (tp-100) REVERT: J 52 TRP cc_start: 0.7979 (t60) cc_final: 0.7349 (t60) REVERT: J 98 ASP cc_start: 0.7458 (m-30) cc_final: 0.7148 (m-30) REVERT: J 117 VAL cc_start: 0.8628 (t) cc_final: 0.8354 (m) REVERT: K 5 THR cc_start: 0.7748 (m) cc_final: 0.7473 (p) REVERT: K 17 GLU cc_start: 0.7848 (mp0) cc_final: 0.6891 (mp0) REVERT: K 90 THR cc_start: 0.8702 (m) cc_final: 0.8391 (p) REVERT: K 94 LEU cc_start: 0.7642 (tp) cc_final: 0.7205 (tt) REVERT: K 99 PHE cc_start: 0.7676 (m-80) cc_final: 0.7179 (m-80) REVERT: h 52 TRP cc_start: 0.8053 (t60) cc_final: 0.7759 (t60) REVERT: h 53 ILE cc_start: 0.8377 (mt) cc_final: 0.8022 (mt) REVERT: h 87 PHE cc_start: 0.8358 (p90) cc_final: 0.8084 (p90) REVERT: h 112 TYR cc_start: 0.8287 (p90) cc_final: 0.7567 (p90) REVERT: l 17 GLU cc_start: 0.7814 (mp0) cc_final: 0.7463 (mp0) REVERT: l 90 THR cc_start: 0.8588 (m) cc_final: 0.8170 (p) REVERT: l 94 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7603 (tt) REVERT: l 99 PHE cc_start: 0.7261 (m-80) cc_final: 0.6585 (m-80) REVERT: l 125 GLU cc_start: 0.6327 (tt0) cc_final: 0.5859 (tt0) outliers start: 59 outliers final: 35 residues processed: 330 average time/residue: 0.1088 time to fit residues: 53.3150 Evaluate side-chains 291 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 419 TYR Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 0.0370 chunk 10 optimal weight: 5.9990 chunk 141 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 149 GLN B 149 GLN c 423 GLN A 149 GLN h 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.105053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.081769 restraints weight = 36895.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085187 restraints weight = 19011.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.087511 restraints weight = 12941.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088934 restraints weight = 10183.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090042 restraints weight = 8777.594| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15642 Z= 0.141 Angle : 0.747 11.283 21390 Z= 0.353 Chirality : 0.042 0.211 2604 Planarity : 0.004 0.039 2514 Dihedral : 5.370 26.091 1902 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.05 % Allowed : 14.62 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.38 (0.21), residues: 1731 helix: 0.86 (0.28), residues: 375 sheet: 0.09 (0.25), residues: 429 loop : -0.87 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 422 TYR 0.023 0.001 TYR a 419 PHE 0.022 0.001 PHE J 87 TRP 0.049 0.002 TRP H 52 HIS 0.005 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (15516) covalent geometry : angle 0.69178 / 0.34 (21039) SS BOND : bond 0.00531 / 0.32 ( 27) SS BOND : angle 2.09092 / 1.22 ( 54) hydrogen bonds : bond 0.03856 / 2.64 ( 552) hydrogen bonds : angle 5.27676 / 3.74 ( 1566) link_ALPHA1-2 : bond 0.00059 / 0.03 ( 3) link_ALPHA1-2 : angle 1.72425 / 0.96 ( 9) link_ALPHA1-3 : bond 0.01684 / 0.77 ( 12) link_ALPHA1-3 : angle 3.56414 / 2.16 ( 36) link_ALPHA1-6 : bond 0.00727 / 0.41 ( 6) link_ALPHA1-6 : angle 1.33919 / 0.78 ( 18) link_BETA1-4 : bond 0.00812 / 0.52 ( 45) link_BETA1-4 : angle 2.45672 / 1.57 ( 135) link_NAG-ASN : bond 0.00367 / 0.22 ( 33) link_NAG-ASN : angle 1.73944 / 1.09 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 296 time to evaluate : 0.571 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: 0.9086 (mmtm) cc_final: 0.8793 (mmmt) REVERT: C 156 ASP cc_start: 0.8157 (t70) cc_final: 0.7141 (t0) REVERT: C 161 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8286 (ttpp) REVERT: C 194 MET cc_start: 0.8923 (tpp) cc_final: 0.8361 (ttp) REVERT: C 214 MET cc_start: 0.8016 (ptp) cc_final: 0.7711 (ptp) REVERT: B 116 LYS cc_start: 0.9145 (mmtm) cc_final: 0.8884 (mmmt) REVERT: B 151 GLU cc_start: 0.8234 (pm20) cc_final: 0.7989 (pm20) REVERT: B 156 ASP cc_start: 0.8076 (t70) cc_final: 0.7750 (t0) REVERT: B 161 LYS cc_start: 0.8595 (ttmt) cc_final: 0.7959 (tptt) REVERT: c 282 ARG cc_start: 0.8478 (tpt90) cc_final: 0.7968 (tpm170) REVERT: c 311 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7885 (t0) REVERT: c 348 GLN cc_start: 0.4595 (mt0) cc_final: 0.3998 (tt0) REVERT: c 420 MET cc_start: 0.7354 (mmt) cc_final: 0.6799 (tpt) REVERT: A 80 MET cc_start: 0.9000 (mmt) cc_final: 0.8352 (mpp) REVERT: A 104 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: A 116 LYS cc_start: 0.9131 (mmtm) cc_final: 0.8872 (mmmt) REVERT: A 134 MET cc_start: 0.9443 (tpp) cc_final: 0.9100 (tpp) REVERT: A 151 GLU cc_start: 0.8292 (pm20) cc_final: 0.8065 (pm20) REVERT: A 161 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8441 (ttpp) REVERT: b 284 MET cc_start: 0.8167 (mtm) cc_final: 0.7692 (mtm) REVERT: b 311 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8090 (t70) REVERT: b 332 MET cc_start: 0.7187 (mmp) cc_final: 0.6740 (tpp) REVERT: b 420 MET cc_start: 0.7607 (mmt) cc_final: 0.6891 (tpt) REVERT: a 282 ARG cc_start: 0.8490 (tpt90) cc_final: 0.7944 (tpm170) REVERT: a 284 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8048 (mtp) REVERT: a 311 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7740 (t0) REVERT: a 326 LEU cc_start: 0.8239 (mt) cc_final: 0.7545 (mt) REVERT: a 348 GLN cc_start: 0.4975 (mt0) cc_final: 0.4163 (tt0) REVERT: a 420 MET cc_start: 0.7969 (mmt) cc_final: 0.7484 (tpt) REVERT: H 6 GLU cc_start: 0.6879 (mm-30) cc_final: 0.5982 (mm-30) REVERT: H 51 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7037 (tt0) REVERT: H 90 LYS cc_start: 0.8423 (mtpt) cc_final: 0.8214 (mtpp) REVERT: H 98 ASP cc_start: 0.7412 (m-30) cc_final: 0.7032 (m-30) REVERT: L 17 GLU cc_start: 0.7490 (mp0) cc_final: 0.7132 (mp0) REVERT: L 18 ARG cc_start: 0.8455 (ttm170) cc_final: 0.7618 (ttp80) REVERT: L 90 THR cc_start: 0.8573 (m) cc_final: 0.8341 (p) REVERT: L 94 LEU cc_start: 0.7845 (tp) cc_final: 0.7187 (tt) REVERT: L 99 PHE cc_start: 0.7243 (m-80) cc_final: 0.6439 (m-80) REVERT: J 5 GLN cc_start: 0.7142 (tp40) cc_final: 0.6829 (tp-100) REVERT: J 43 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7913 (mtm110) REVERT: J 52 TRP cc_start: 0.7971 (t60) cc_final: 0.7267 (t60) REVERT: J 98 ASP cc_start: 0.7144 (m-30) cc_final: 0.6617 (m-30) REVERT: K 17 GLU cc_start: 0.7927 (mp0) cc_final: 0.6956 (mp0) REVERT: K 42 TYR cc_start: 0.8638 (m-80) cc_final: 0.7852 (m-80) REVERT: K 90 THR cc_start: 0.8722 (m) cc_final: 0.8464 (p) REVERT: K 94 LEU cc_start: 0.7615 (tp) cc_final: 0.7189 (tt) REVERT: K 99 PHE cc_start: 0.7592 (m-80) cc_final: 0.6942 (m-80) REVERT: h 52 TRP cc_start: 0.7957 (t60) cc_final: 0.7591 (t60) REVERT: h 53 ILE cc_start: 0.8303 (mt) cc_final: 0.8027 (mt) REVERT: h 87 PHE cc_start: 0.8428 (p90) cc_final: 0.7993 (p90) REVERT: h 112 TYR cc_start: 0.8027 (p90) cc_final: 0.7065 (p90) REVERT: l 17 GLU cc_start: 0.7887 (mp0) cc_final: 0.7531 (mp0) REVERT: l 90 THR cc_start: 0.8622 (m) cc_final: 0.8253 (p) REVERT: l 94 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7525 (tt) REVERT: l 99 PHE cc_start: 0.7132 (m-80) cc_final: 0.6377 (m-80) REVERT: l 125 GLU cc_start: 0.6129 (tt0) cc_final: 0.5827 (tt0) outliers start: 47 outliers final: 26 residues processed: 324 average time/residue: 0.1277 time to fit residues: 60.8890 Evaluate side-chains 287 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 255 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 121 optimal weight: 0.0020 chunk 165 optimal weight: 0.0040 chunk 106 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.106283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.082163 restraints weight = 37849.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085652 restraints weight = 20187.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087975 restraints weight = 13956.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089502 restraints weight = 11122.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.090451 restraints weight = 9556.284| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15642 Z= 0.130 Angle : 0.712 10.295 21390 Z= 0.338 Chirality : 0.041 0.209 2604 Planarity : 0.004 0.053 2514 Dihedral : 5.180 26.983 1902 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.18 % Allowed : 15.53 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.31 (0.21), residues: 1731 helix: 1.03 (0.28), residues: 375 sheet: 0.12 (0.25), residues: 429 loop : -0.87 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG l 67 TYR 0.022 0.001 TYR a 419 PHE 0.021 0.001 PHE J 30 TRP 0.052 0.001 TRP H 52 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (15516) covalent geometry : angle 0.66017 / 0.33 (21039) SS BOND : bond 0.00587 / 0.38 ( 27) SS BOND : angle 1.89070 / 1.11 ( 54) hydrogen bonds : bond 0.03568 / 2.42 ( 552) hydrogen bonds : angle 5.11804 / 3.63 ( 1566) link_ALPHA1-2 : bond 0.00107 / 0.05 ( 3) link_ALPHA1-2 : angle 1.69273 / 0.95 ( 9) link_ALPHA1-3 : bond 0.01592 / 0.74 ( 12) link_ALPHA1-3 : angle 3.46775 / 2.10 ( 36) link_ALPHA1-6 : bond 0.00773 / 0.43 ( 6) link_ALPHA1-6 : angle 1.29662 / 0.75 ( 18) link_BETA1-4 : bond 0.00764 / 0.49 ( 45) link_BETA1-4 : angle 2.32645 / 1.48 ( 135) link_NAG-ASN : bond 0.00277 / 0.17 ( 33) link_NAG-ASN : angle 1.59558 / 1.00 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 283 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.8530 (ptt) cc_final: 0.8169 (pmm) REVERT: C 116 LYS cc_start: 0.9131 (mmtm) cc_final: 0.8811 (mmmt) REVERT: C 156 ASP cc_start: 0.8178 (t70) cc_final: 0.7601 (t0) REVERT: C 161 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8128 (tptt) REVERT: C 194 MET cc_start: 0.8943 (tpp) cc_final: 0.8352 (ttp) REVERT: C 214 MET cc_start: 0.8023 (ptp) cc_final: 0.7737 (ptp) REVERT: B 116 LYS cc_start: 0.9174 (mmtm) cc_final: 0.8932 (mmmt) REVERT: B 151 GLU cc_start: 0.8199 (pm20) cc_final: 0.7948 (pm20) REVERT: B 156 ASP cc_start: 0.8042 (t70) cc_final: 0.7687 (t0) REVERT: B 161 LYS cc_start: 0.8561 (ttmt) cc_final: 0.7938 (tptt) REVERT: c 282 ARG cc_start: 0.8509 (tpt90) cc_final: 0.8006 (tpm170) REVERT: c 311 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7859 (t0) REVERT: c 326 LEU cc_start: 0.8340 (mp) cc_final: 0.7843 (tp) REVERT: c 348 GLN cc_start: 0.4799 (mt0) cc_final: 0.4116 (tt0) REVERT: c 420 MET cc_start: 0.7684 (mmt) cc_final: 0.7110 (tpt) REVERT: A 116 LYS cc_start: 0.9148 (mmtm) cc_final: 0.8907 (mmmt) REVERT: A 134 MET cc_start: 0.9437 (tpp) cc_final: 0.9084 (tpp) REVERT: A 151 GLU cc_start: 0.8199 (pm20) cc_final: 0.7962 (pm20) REVERT: A 161 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8465 (ttpp) REVERT: A 194 MET cc_start: 0.8741 (tpp) cc_final: 0.8133 (ttm) REVERT: b 311 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8205 (t70) REVERT: b 326 LEU cc_start: 0.8312 (mp) cc_final: 0.7860 (tp) REVERT: b 332 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6793 (tpp) REVERT: b 419 TYR cc_start: 0.7258 (t80) cc_final: 0.6785 (t80) REVERT: b 420 MET cc_start: 0.7676 (mmt) cc_final: 0.6732 (tpt) REVERT: a 282 ARG cc_start: 0.8406 (tpt90) cc_final: 0.7842 (tpm170) REVERT: a 284 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8068 (mtp) REVERT: a 311 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7914 (t0) REVERT: a 326 LEU cc_start: 0.8322 (mt) cc_final: 0.7447 (mt) REVERT: a 348 GLN cc_start: 0.4789 (mt0) cc_final: 0.4068 (tt0) REVERT: a 410 MET cc_start: 0.7848 (mtp) cc_final: 0.7498 (ttm) REVERT: a 420 MET cc_start: 0.7969 (mmt) cc_final: 0.7531 (tpt) REVERT: H 5 GLN cc_start: 0.7111 (tp40) cc_final: 0.6813 (tp-100) REVERT: H 51 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6964 (tt0) REVERT: H 90 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8274 (mtpp) REVERT: H 98 ASP cc_start: 0.7321 (m-30) cc_final: 0.6900 (m-30) REVERT: L 17 GLU cc_start: 0.7443 (mp0) cc_final: 0.7116 (mp0) REVERT: L 18 ARG cc_start: 0.8478 (ttm170) cc_final: 0.7593 (ttp80) REVERT: L 94 LEU cc_start: 0.7785 (tp) cc_final: 0.7120 (tt) REVERT: L 99 PHE cc_start: 0.7218 (m-80) cc_final: 0.6493 (m-80) REVERT: L 102 TYR cc_start: 0.8173 (m-80) cc_final: 0.7875 (m-80) REVERT: J 5 GLN cc_start: 0.7004 (tp40) cc_final: 0.6636 (tp-100) REVERT: J 6 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7428 (mm-30) REVERT: J 43 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7872 (mtm110) REVERT: J 52 TRP cc_start: 0.7955 (t60) cc_final: 0.7577 (t60) REVERT: J 98 ASP cc_start: 0.6998 (m-30) cc_final: 0.6590 (m-30) REVERT: K 17 GLU cc_start: 0.8074 (mp0) cc_final: 0.7206 (mp0) REVERT: K 42 TYR cc_start: 0.8458 (m-80) cc_final: 0.7743 (m-80) REVERT: K 90 THR cc_start: 0.8676 (m) cc_final: 0.8431 (p) REVERT: K 94 LEU cc_start: 0.7666 (tp) cc_final: 0.7239 (tt) REVERT: K 99 PHE cc_start: 0.7554 (m-80) cc_final: 0.6945 (m-80) REVERT: h 5 GLN cc_start: 0.6740 (tp40) cc_final: 0.6412 (tp-100) REVERT: h 52 TRP cc_start: 0.7960 (t60) cc_final: 0.7534 (t60) REVERT: h 53 ILE cc_start: 0.8294 (mt) cc_final: 0.8001 (mt) REVERT: h 85 ASN cc_start: 0.7286 (p0) cc_final: 0.7015 (p0) REVERT: h 87 PHE cc_start: 0.8419 (p90) cc_final: 0.8035 (p90) REVERT: h 110 TYR cc_start: 0.8245 (t80) cc_final: 0.7969 (t80) REVERT: h 112 TYR cc_start: 0.8027 (p90) cc_final: 0.6908 (p90) REVERT: l 17 GLU cc_start: 0.7884 (mp0) cc_final: 0.7526 (mp0) REVERT: l 90 THR cc_start: 0.8642 (m) cc_final: 0.8285 (p) REVERT: l 94 LEU cc_start: 0.7779 (tt) cc_final: 0.7442 (tt) REVERT: l 99 PHE cc_start: 0.7222 (m-80) cc_final: 0.6525 (m-80) outliers start: 49 outliers final: 30 residues processed: 312 average time/residue: 0.1247 time to fit residues: 58.0183 Evaluate side-chains 290 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 72 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 45 optimal weight: 0.0170 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.103954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080823 restraints weight = 36686.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.084118 restraints weight = 19157.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086353 restraints weight = 13198.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087823 restraints weight = 10439.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088823 restraints weight = 8976.225| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15642 Z= 0.159 Angle : 0.723 10.507 21390 Z= 0.339 Chirality : 0.041 0.187 2604 Planarity : 0.004 0.043 2514 Dihedral : 5.085 23.916 1902 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.18 % Allowed : 15.27 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.30 (0.21), residues: 1731 helix: 1.11 (0.29), residues: 375 sheet: 0.07 (0.25), residues: 432 loop : -0.87 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 67 TYR 0.025 0.001 TYR a 419 PHE 0.012 0.001 PHE H 87 TRP 0.036 0.001 TRP H 52 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (15516) covalent geometry : angle 0.67398 / 0.33 (21039) SS BOND : bond 0.00669 / 0.42 ( 27) SS BOND : angle 1.73617 / 1.03 ( 54) hydrogen bonds : bond 0.03688 / 2.49 ( 552) hydrogen bonds : angle 5.03565 / 3.57 ( 1566) link_ALPHA1-2 : bond 0.00066 / 0.03 ( 3) link_ALPHA1-2 : angle 1.67089 / 0.93 ( 9) link_ALPHA1-3 : bond 0.01564 / 0.70 ( 12) link_ALPHA1-3 : angle 3.50713 / 2.13 ( 36) link_ALPHA1-6 : bond 0.00661 / 0.37 ( 6) link_ALPHA1-6 : angle 1.36859 / 0.80 ( 18) link_BETA1-4 : bond 0.00712 / 0.46 ( 45) link_BETA1-4 : angle 2.30124 / 1.46 ( 135) link_NAG-ASN : bond 0.00240 / 0.16 ( 33) link_NAG-ASN : angle 1.58644 / 1.00 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7252 (mp0) cc_final: 0.6925 (mp0) REVERT: C 82 MET cc_start: 0.8512 (ptt) cc_final: 0.8283 (pmm) REVERT: C 156 ASP cc_start: 0.8235 (t70) cc_final: 0.7645 (t0) REVERT: C 161 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8171 (tptt) REVERT: C 194 MET cc_start: 0.8982 (tpp) cc_final: 0.8315 (ttp) REVERT: C 214 MET cc_start: 0.8036 (ptp) cc_final: 0.7772 (ptp) REVERT: B 116 LYS cc_start: 0.9171 (mmtm) cc_final: 0.8935 (mmmt) REVERT: B 156 ASP cc_start: 0.8061 (t70) cc_final: 0.7690 (t0) REVERT: B 161 LYS cc_start: 0.8600 (ttmt) cc_final: 0.7960 (tptt) REVERT: c 282 ARG cc_start: 0.8573 (tpt90) cc_final: 0.7956 (tpm170) REVERT: c 311 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8024 (t0) REVERT: c 332 MET cc_start: 0.7760 (tpp) cc_final: 0.7380 (tpp) REVERT: c 348 GLN cc_start: 0.4835 (mt0) cc_final: 0.4137 (tt0) REVERT: c 420 MET cc_start: 0.7713 (mmt) cc_final: 0.7087 (tpt) REVERT: A 82 MET cc_start: 0.8953 (pmm) cc_final: 0.8235 (pmm) REVERT: A 116 LYS cc_start: 0.9185 (mmtm) cc_final: 0.8967 (mmmt) REVERT: A 134 MET cc_start: 0.9436 (tpp) cc_final: 0.9055 (tpp) REVERT: A 161 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8424 (ttpp) REVERT: b 284 MET cc_start: 0.8227 (mtm) cc_final: 0.7523 (mtm) REVERT: b 332 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6778 (tpp) REVERT: b 351 MET cc_start: 0.9061 (tpp) cc_final: 0.8747 (mmm) REVERT: b 419 TYR cc_start: 0.7157 (t80) cc_final: 0.6773 (t80) REVERT: b 420 MET cc_start: 0.7624 (mmt) cc_final: 0.6654 (tpt) REVERT: a 282 ARG cc_start: 0.8437 (tpt90) cc_final: 0.7997 (tpt170) REVERT: a 284 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8169 (mtp) REVERT: a 311 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7873 (t70) REVERT: a 348 GLN cc_start: 0.4864 (mt0) cc_final: 0.3926 (tt0) REVERT: a 410 MET cc_start: 0.7901 (mtp) cc_final: 0.7446 (ttm) REVERT: a 420 MET cc_start: 0.8047 (mmt) cc_final: 0.7560 (tpt) REVERT: H 5 GLN cc_start: 0.7361 (tp40) cc_final: 0.7041 (tp-100) REVERT: H 6 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7113 (mm-30) REVERT: H 51 GLU cc_start: 0.7228 (mt-10) cc_final: 0.7017 (tt0) REVERT: H 90 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8264 (mtpp) REVERT: H 98 ASP cc_start: 0.7445 (m-30) cc_final: 0.7040 (m-30) REVERT: L 17 GLU cc_start: 0.7507 (mp0) cc_final: 0.7171 (mp0) REVERT: L 18 ARG cc_start: 0.8516 (ttm170) cc_final: 0.7555 (ttp80) REVERT: L 94 LEU cc_start: 0.7758 (tp) cc_final: 0.7109 (tt) REVERT: L 99 PHE cc_start: 0.7337 (m-80) cc_final: 0.6647 (m-80) REVERT: J 5 GLN cc_start: 0.7031 (tp40) cc_final: 0.6705 (tp-100) REVERT: J 43 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7848 (mtm110) REVERT: J 52 TRP cc_start: 0.7881 (t60) cc_final: 0.7494 (t60) REVERT: J 98 ASP cc_start: 0.7107 (m-30) cc_final: 0.6687 (m-30) REVERT: K 17 GLU cc_start: 0.8182 (mp0) cc_final: 0.7344 (mp0) REVERT: K 42 TYR cc_start: 0.8505 (m-80) cc_final: 0.7875 (m-80) REVERT: K 90 THR cc_start: 0.8760 (m) cc_final: 0.8509 (p) REVERT: K 94 LEU cc_start: 0.7680 (tp) cc_final: 0.7228 (tt) REVERT: K 99 PHE cc_start: 0.7588 (m-80) cc_final: 0.7019 (m-80) REVERT: K 102 TYR cc_start: 0.7972 (m-80) cc_final: 0.7625 (m-80) REVERT: h 5 GLN cc_start: 0.6838 (tp40) cc_final: 0.6423 (tp-100) REVERT: h 52 TRP cc_start: 0.8031 (t60) cc_final: 0.7530 (t60) REVERT: h 53 ILE cc_start: 0.8271 (mt) cc_final: 0.7862 (mt) REVERT: h 85 ASN cc_start: 0.7239 (p0) cc_final: 0.6960 (p0) REVERT: h 87 PHE cc_start: 0.8460 (p90) cc_final: 0.8050 (p90) REVERT: h 110 TYR cc_start: 0.8298 (t80) cc_final: 0.8018 (t80) REVERT: l 17 GLU cc_start: 0.7902 (mp0) cc_final: 0.7543 (mp0) REVERT: l 90 THR cc_start: 0.8710 (m) cc_final: 0.8338 (p) REVERT: l 94 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7489 (tt) REVERT: l 99 PHE cc_start: 0.7240 (m-80) cc_final: 0.6607 (m-80) outliers start: 49 outliers final: 34 residues processed: 295 average time/residue: 0.1302 time to fit residues: 56.7858 Evaluate side-chains 285 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 64 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080186 restraints weight = 37465.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083535 restraints weight = 19193.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085742 restraints weight = 13139.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087209 restraints weight = 10430.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088185 restraints weight = 8954.272| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15642 Z= 0.164 Angle : 0.734 10.230 21390 Z= 0.344 Chirality : 0.042 0.216 2604 Planarity : 0.004 0.049 2514 Dihedral : 5.045 22.832 1902 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.05 % Allowed : 16.24 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.31 (0.21), residues: 1731 helix: 1.16 (0.29), residues: 375 sheet: 0.14 (0.25), residues: 426 loop : -0.95 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 67 TYR 0.020 0.001 TYR a 419 PHE 0.023 0.002 PHE J 30 TRP 0.038 0.001 TRP H 52 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15516) covalent geometry : angle 0.68638 / 0.33 (21039) SS BOND : bond 0.00927 / 0.67 ( 27) SS BOND : angle 1.75757 / 1.06 ( 54) hydrogen bonds : bond 0.03604 / 2.42 ( 552) hydrogen bonds : angle 5.03204 / 3.57 ( 1566) link_ALPHA1-2 : bond 0.00051 / 0.03 ( 3) link_ALPHA1-2 : angle 1.66979 / 0.94 ( 9) link_ALPHA1-3 : bond 0.01559 / 0.69 ( 12) link_ALPHA1-3 : angle 3.51419 / 2.13 ( 36) link_ALPHA1-6 : bond 0.00657 / 0.36 ( 6) link_ALPHA1-6 : angle 1.40961 / 0.82 ( 18) link_BETA1-4 : bond 0.00728 / 0.47 ( 45) link_BETA1-4 : angle 2.26010 / 1.44 ( 135) link_NAG-ASN : bond 0.00239 / 0.15 ( 33) link_NAG-ASN : angle 1.57338 / 0.99 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7244 (mp0) cc_final: 0.6965 (mp0) REVERT: C 82 MET cc_start: 0.8668 (ptt) cc_final: 0.8216 (pmm) REVERT: C 156 ASP cc_start: 0.8223 (t70) cc_final: 0.7342 (t0) REVERT: C 161 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8361 (ttpp) REVERT: C 194 MET cc_start: 0.8979 (tpp) cc_final: 0.8300 (ttp) REVERT: B 116 LYS cc_start: 0.9165 (mmtm) cc_final: 0.8936 (mmmt) REVERT: B 156 ASP cc_start: 0.8073 (t70) cc_final: 0.7701 (t0) REVERT: B 161 LYS cc_start: 0.8614 (ttmt) cc_final: 0.7969 (tptt) REVERT: B 194 MET cc_start: 0.8768 (tpp) cc_final: 0.8222 (ttp) REVERT: c 282 ARG cc_start: 0.8677 (tpt90) cc_final: 0.8076 (tpm170) REVERT: c 311 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7966 (t0) REVERT: c 332 MET cc_start: 0.7717 (tpp) cc_final: 0.7150 (tpp) REVERT: c 348 GLN cc_start: 0.4964 (mt0) cc_final: 0.4189 (tt0) REVERT: c 420 MET cc_start: 0.7615 (mmt) cc_final: 0.7271 (tpt) REVERT: A 116 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8967 (mmmt) REVERT: A 134 MET cc_start: 0.9439 (tpp) cc_final: 0.9076 (tpp) REVERT: A 156 ASP cc_start: 0.8004 (p0) cc_final: 0.7802 (p0) REVERT: A 161 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8372 (ttpp) REVERT: A 194 MET cc_start: 0.8771 (tpp) cc_final: 0.8131 (ttm) REVERT: b 284 MET cc_start: 0.8281 (mtm) cc_final: 0.7588 (mtm) REVERT: b 306 ASP cc_start: 0.8126 (p0) cc_final: 0.7874 (p0) REVERT: b 332 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6736 (tpp) REVERT: b 351 MET cc_start: 0.9049 (tpp) cc_final: 0.8727 (mmm) REVERT: b 419 TYR cc_start: 0.7369 (t80) cc_final: 0.6829 (t80) REVERT: b 420 MET cc_start: 0.7519 (mmt) cc_final: 0.6608 (tpt) REVERT: a 282 ARG cc_start: 0.8466 (tpt90) cc_final: 0.8010 (tpt170) REVERT: a 284 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8055 (mtp) REVERT: a 311 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7887 (t0) REVERT: a 332 MET cc_start: 0.7683 (tpp) cc_final: 0.6968 (tpp) REVERT: a 348 GLN cc_start: 0.4679 (mt0) cc_final: 0.4122 (tt0) REVERT: a 410 MET cc_start: 0.7892 (mtp) cc_final: 0.7437 (ttm) REVERT: a 420 MET cc_start: 0.8005 (mmt) cc_final: 0.7640 (tpt) REVERT: a 423 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7188 (mp10) REVERT: H 5 GLN cc_start: 0.7334 (tp40) cc_final: 0.6949 (tp-100) REVERT: H 51 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7080 (tt0) REVERT: H 90 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8264 (mtpp) REVERT: H 95 THR cc_start: 0.7963 (t) cc_final: 0.7631 (p) REVERT: H 98 ASP cc_start: 0.7476 (m-30) cc_final: 0.7046 (m-30) REVERT: L 17 GLU cc_start: 0.7505 (mp0) cc_final: 0.7172 (mp0) REVERT: L 18 ARG cc_start: 0.8490 (ttm170) cc_final: 0.7554 (ttp80) REVERT: L 94 LEU cc_start: 0.7757 (tp) cc_final: 0.7141 (tt) REVERT: L 99 PHE cc_start: 0.7407 (m-80) cc_final: 0.6795 (m-80) REVERT: L 102 TYR cc_start: 0.8192 (m-80) cc_final: 0.7860 (m-80) REVERT: J 5 GLN cc_start: 0.7030 (tp40) cc_final: 0.6669 (tp-100) REVERT: J 43 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7911 (mtm110) REVERT: J 52 TRP cc_start: 0.7995 (t60) cc_final: 0.7570 (t60) REVERT: J 98 ASP cc_start: 0.7138 (m-30) cc_final: 0.6736 (m-30) REVERT: K 17 GLU cc_start: 0.8251 (mp0) cc_final: 0.7347 (mp0) REVERT: K 42 TYR cc_start: 0.8504 (m-80) cc_final: 0.7777 (m-80) REVERT: K 90 THR cc_start: 0.8769 (m) cc_final: 0.8482 (p) REVERT: K 94 LEU cc_start: 0.7415 (tp) cc_final: 0.6944 (tt) REVERT: K 99 PHE cc_start: 0.7514 (m-80) cc_final: 0.6872 (m-80) REVERT: K 102 TYR cc_start: 0.7927 (m-80) cc_final: 0.7603 (m-80) REVERT: h 5 GLN cc_start: 0.6879 (tp40) cc_final: 0.6476 (tp-100) REVERT: h 52 TRP cc_start: 0.8028 (t60) cc_final: 0.7525 (t60) REVERT: h 53 ILE cc_start: 0.8301 (mt) cc_final: 0.7889 (mt) REVERT: h 87 PHE cc_start: 0.8439 (p90) cc_final: 0.7962 (p90) REVERT: l 17 GLU cc_start: 0.7925 (mp0) cc_final: 0.7571 (mp0) REVERT: l 90 THR cc_start: 0.8734 (m) cc_final: 0.8349 (p) REVERT: l 94 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7537 (tt) REVERT: l 99 PHE cc_start: 0.7288 (m-80) cc_final: 0.6694 (m-80) outliers start: 47 outliers final: 33 residues processed: 282 average time/residue: 0.1317 time to fit residues: 55.0055 Evaluate side-chains 284 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain a residue 423 GLN Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 43 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 14 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.102774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079728 restraints weight = 37412.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083052 restraints weight = 19135.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085273 restraints weight = 13102.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086726 restraints weight = 10374.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087689 restraints weight = 8923.329| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15642 Z= 0.172 Angle : 0.742 10.156 21390 Z= 0.348 Chirality : 0.042 0.182 2604 Planarity : 0.004 0.056 2514 Dihedral : 5.037 21.559 1902 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.08 % Favored : 94.74 % Rotamer: Outliers : 2.79 % Allowed : 17.35 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.36 (0.21), residues: 1731 helix: 1.17 (0.28), residues: 375 sheet: 0.12 (0.25), residues: 426 loop : -1.00 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 67 TYR 0.019 0.001 TYR a 419 PHE 0.012 0.001 PHE H 87 TRP 0.036 0.001 TRP H 52 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (15516) covalent geometry : angle 0.69564 / 0.34 (21039) SS BOND : bond 0.00698 / 0.45 ( 27) SS BOND : angle 1.72031 / 1.03 ( 54) hydrogen bonds : bond 0.03707 / 2.48 ( 552) hydrogen bonds : angle 5.04527 / 3.58 ( 1566) link_ALPHA1-2 : bond 0.00045 / 0.02 ( 3) link_ALPHA1-2 : angle 1.67650 / 0.94 ( 9) link_ALPHA1-3 : bond 0.01569 / 0.69 ( 12) link_ALPHA1-3 : angle 3.46707 / 2.10 ( 36) link_ALPHA1-6 : bond 0.00635 / 0.35 ( 6) link_ALPHA1-6 : angle 1.39994 / 0.81 ( 18) link_BETA1-4 : bond 0.00690 / 0.44 ( 45) link_BETA1-4 : angle 2.24352 / 1.43 ( 135) link_NAG-ASN : bond 0.00230 / 0.15 ( 33) link_NAG-ASN : angle 1.59156 / 1.00 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7316 (mp0) cc_final: 0.6988 (mp0) REVERT: C 151 GLU cc_start: 0.8304 (pm20) cc_final: 0.7963 (pm20) REVERT: C 156 ASP cc_start: 0.8204 (t70) cc_final: 0.7354 (t0) REVERT: C 161 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8375 (ttpp) REVERT: C 194 MET cc_start: 0.9001 (tpp) cc_final: 0.8331 (ttp) REVERT: B 116 LYS cc_start: 0.9169 (mmtm) cc_final: 0.8949 (mmmt) REVERT: B 156 ASP cc_start: 0.8031 (t70) cc_final: 0.7394 (t0) REVERT: B 161 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8311 (ttpp) REVERT: B 251 ASP cc_start: 0.7389 (m-30) cc_final: 0.7139 (m-30) REVERT: c 282 ARG cc_start: 0.8669 (tpt90) cc_final: 0.8114 (tpm170) REVERT: c 311 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7979 (t0) REVERT: c 332 MET cc_start: 0.7702 (tpp) cc_final: 0.7002 (tpp) REVERT: c 348 GLN cc_start: 0.5153 (mt0) cc_final: 0.4289 (tt0) REVERT: c 420 MET cc_start: 0.7760 (mmt) cc_final: 0.7266 (tpt) REVERT: A 116 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8989 (mmmt) REVERT: A 125 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8682 (tppt) REVERT: A 134 MET cc_start: 0.9463 (tpp) cc_final: 0.9100 (tpp) REVERT: A 151 GLU cc_start: 0.8006 (pm20) cc_final: 0.7786 (pt0) REVERT: A 161 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8420 (ttpp) REVERT: b 284 MET cc_start: 0.8285 (mtm) cc_final: 0.7611 (mtm) REVERT: b 351 MET cc_start: 0.9076 (tpp) cc_final: 0.8739 (mmm) REVERT: b 419 TYR cc_start: 0.7501 (t80) cc_final: 0.7253 (t80) REVERT: b 420 MET cc_start: 0.7600 (mmt) cc_final: 0.6922 (tpt) REVERT: a 282 ARG cc_start: 0.8523 (tpt90) cc_final: 0.8055 (tpt170) REVERT: a 284 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8062 (mtp) REVERT: a 311 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7902 (t0) REVERT: a 332 MET cc_start: 0.7708 (tpp) cc_final: 0.6896 (tpp) REVERT: a 348 GLN cc_start: 0.4709 (mt0) cc_final: 0.4173 (tt0) REVERT: a 410 MET cc_start: 0.7948 (mtp) cc_final: 0.7427 (ttm) REVERT: a 420 MET cc_start: 0.8045 (mmt) cc_final: 0.7700 (tpt) REVERT: a 423 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: H 51 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7207 (tt0) REVERT: H 90 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8327 (mtpp) REVERT: H 95 THR cc_start: 0.8070 (t) cc_final: 0.7776 (p) REVERT: H 98 ASP cc_start: 0.7552 (m-30) cc_final: 0.7124 (m-30) REVERT: L 17 GLU cc_start: 0.7523 (mp0) cc_final: 0.7188 (mp0) REVERT: L 18 ARG cc_start: 0.8465 (ttm170) cc_final: 0.7516 (ttp80) REVERT: L 94 LEU cc_start: 0.7741 (tp) cc_final: 0.7108 (tt) REVERT: L 99 PHE cc_start: 0.7442 (m-80) cc_final: 0.6841 (m-80) REVERT: L 127 LYS cc_start: 0.7540 (pttt) cc_final: 0.7280 (ptpt) REVERT: J 5 GLN cc_start: 0.7072 (tp40) cc_final: 0.6724 (tp-100) REVERT: J 43 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7963 (mtm110) REVERT: J 52 TRP cc_start: 0.8014 (t60) cc_final: 0.7623 (t60) REVERT: J 98 ASP cc_start: 0.7249 (m-30) cc_final: 0.6849 (m-30) REVERT: K 17 GLU cc_start: 0.8290 (mp0) cc_final: 0.7386 (mp0) REVERT: K 42 TYR cc_start: 0.8531 (m-80) cc_final: 0.7797 (m-80) REVERT: K 90 THR cc_start: 0.8824 (m) cc_final: 0.8530 (p) REVERT: K 94 LEU cc_start: 0.7659 (tp) cc_final: 0.7197 (tt) REVERT: K 99 PHE cc_start: 0.7512 (m-80) cc_final: 0.6902 (m-80) REVERT: h 5 GLN cc_start: 0.7026 (tp40) cc_final: 0.6638 (tp-100) REVERT: h 52 TRP cc_start: 0.8078 (t60) cc_final: 0.7555 (t60) REVERT: h 53 ILE cc_start: 0.8336 (mt) cc_final: 0.7920 (mt) REVERT: h 85 ASN cc_start: 0.7884 (p0) cc_final: 0.7285 (p0) REVERT: h 87 PHE cc_start: 0.8491 (p90) cc_final: 0.8068 (p90) REVERT: l 17 GLU cc_start: 0.7953 (mp0) cc_final: 0.7599 (mp0) REVERT: l 90 THR cc_start: 0.8783 (m) cc_final: 0.8384 (p) REVERT: l 94 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7558 (tt) REVERT: l 99 PHE cc_start: 0.7313 (m-80) cc_final: 0.6700 (m-80) outliers start: 43 outliers final: 30 residues processed: 280 average time/residue: 0.1319 time to fit residues: 54.4337 Evaluate side-chains 282 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain a residue 423 GLN Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 160 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079071 restraints weight = 37946.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.082400 restraints weight = 19541.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084619 restraints weight = 13381.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086081 restraints weight = 10602.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087015 restraints weight = 9128.719| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15642 Z= 0.176 Angle : 0.750 10.627 21390 Z= 0.351 Chirality : 0.042 0.180 2604 Planarity : 0.004 0.056 2514 Dihedral : 5.056 22.056 1902 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 2.66 % Allowed : 17.41 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.43 (0.21), residues: 1731 helix: 1.20 (0.28), residues: 375 sheet: 0.08 (0.25), residues: 423 loop : -1.08 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 67 TYR 0.021 0.001 TYR a 419 PHE 0.016 0.002 PHE l 76 TRP 0.039 0.002 TRP H 52 HIS 0.004 0.001 HIS a 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (15516) covalent geometry : angle 0.70408 / 0.34 (21039) SS BOND : bond 0.00723 / 0.46 ( 27) SS BOND : angle 1.82849 / 1.07 ( 54) hydrogen bonds : bond 0.03765 / 2.52 ( 552) hydrogen bonds : angle 5.06836 / 3.59 ( 1566) link_ALPHA1-2 : bond 0.00034 / 0.02 ( 3) link_ALPHA1-2 : angle 1.69043 / 0.95 ( 9) link_ALPHA1-3 : bond 0.01523 / 0.68 ( 12) link_ALPHA1-3 : angle 3.53098 / 2.14 ( 36) link_ALPHA1-6 : bond 0.00622 / 0.34 ( 6) link_ALPHA1-6 : angle 1.38278 / 0.80 ( 18) link_BETA1-4 : bond 0.00684 / 0.44 ( 45) link_BETA1-4 : angle 2.22011 / 1.41 ( 135) link_NAG-ASN : bond 0.00239 / 0.16 ( 33) link_NAG-ASN : angle 1.63098 / 1.03 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7338 (mp0) cc_final: 0.7052 (mp0) REVERT: C 151 GLU cc_start: 0.8263 (pm20) cc_final: 0.7890 (pm20) REVERT: C 156 ASP cc_start: 0.8241 (t70) cc_final: 0.7388 (t0) REVERT: C 161 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8374 (ttpp) REVERT: C 194 MET cc_start: 0.9008 (tpp) cc_final: 0.8353 (ttp) REVERT: B 116 LYS cc_start: 0.9155 (mmtm) cc_final: 0.8938 (mmmt) REVERT: B 156 ASP cc_start: 0.8072 (t70) cc_final: 0.7408 (t0) REVERT: B 161 LYS cc_start: 0.8688 (ttmt) cc_final: 0.8257 (ttpp) REVERT: B 194 MET cc_start: 0.8794 (tpp) cc_final: 0.8201 (ttp) REVERT: c 282 ARG cc_start: 0.8692 (tpt90) cc_final: 0.8120 (tpm170) REVERT: c 311 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.8000 (t0) REVERT: c 332 MET cc_start: 0.7690 (tpp) cc_final: 0.7021 (tpp) REVERT: c 348 GLN cc_start: 0.5022 (mt0) cc_final: 0.4367 (tt0) REVERT: c 420 MET cc_start: 0.7716 (mmt) cc_final: 0.7231 (tpt) REVERT: A 116 LYS cc_start: 0.9194 (mmtm) cc_final: 0.8987 (mmmt) REVERT: A 125 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8695 (tppt) REVERT: A 134 MET cc_start: 0.9454 (tpp) cc_final: 0.9100 (tpp) REVERT: A 151 GLU cc_start: 0.8032 (pm20) cc_final: 0.7699 (pt0) REVERT: A 161 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8499 (ttpp) REVERT: A 194 MET cc_start: 0.8760 (tpp) cc_final: 0.8165 (ttm) REVERT: b 284 MET cc_start: 0.8328 (mtm) cc_final: 0.7612 (mtm) REVERT: b 351 MET cc_start: 0.9030 (tpp) cc_final: 0.8690 (mmm) REVERT: b 419 TYR cc_start: 0.7480 (t80) cc_final: 0.6905 (t80) REVERT: b 420 MET cc_start: 0.7640 (mmt) cc_final: 0.6803 (tpt) REVERT: a 284 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: a 311 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7885 (t0) REVERT: a 332 MET cc_start: 0.7724 (tpp) cc_final: 0.6930 (tpp) REVERT: a 348 GLN cc_start: 0.4653 (mt0) cc_final: 0.3732 (tt0) REVERT: a 410 MET cc_start: 0.8002 (mtp) cc_final: 0.7488 (ttm) REVERT: a 420 MET cc_start: 0.8163 (mmt) cc_final: 0.7827 (tpt) REVERT: a 423 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: H 51 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7274 (tt0) REVERT: H 90 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8328 (mtpp) REVERT: H 95 THR cc_start: 0.8209 (t) cc_final: 0.7914 (p) REVERT: H 98 ASP cc_start: 0.7462 (m-30) cc_final: 0.7064 (m-30) REVERT: L 17 GLU cc_start: 0.7494 (mp0) cc_final: 0.7167 (mp0) REVERT: L 18 ARG cc_start: 0.8463 (ttm170) cc_final: 0.7466 (ttp80) REVERT: L 94 LEU cc_start: 0.7730 (tp) cc_final: 0.7086 (tt) REVERT: L 99 PHE cc_start: 0.7507 (m-80) cc_final: 0.6867 (m-80) REVERT: L 102 TYR cc_start: 0.8263 (m-80) cc_final: 0.7933 (m-80) REVERT: J 5 GLN cc_start: 0.7086 (tp40) cc_final: 0.6734 (tp-100) REVERT: J 52 TRP cc_start: 0.7974 (t60) cc_final: 0.7582 (t60) REVERT: J 98 ASP cc_start: 0.7279 (m-30) cc_final: 0.6854 (m-30) REVERT: K 17 GLU cc_start: 0.8277 (mp0) cc_final: 0.7412 (mp0) REVERT: K 42 TYR cc_start: 0.8564 (m-80) cc_final: 0.7755 (m-80) REVERT: K 90 THR cc_start: 0.8869 (m) cc_final: 0.8577 (p) REVERT: K 94 LEU cc_start: 0.7412 (tp) cc_final: 0.6928 (tt) REVERT: K 99 PHE cc_start: 0.7540 (m-80) cc_final: 0.6797 (m-80) REVERT: K 102 TYR cc_start: 0.7987 (m-80) cc_final: 0.7710 (m-80) REVERT: h 5 GLN cc_start: 0.7093 (tp40) cc_final: 0.6718 (tp-100) REVERT: h 53 ILE cc_start: 0.8282 (mt) cc_final: 0.8017 (mt) REVERT: h 87 PHE cc_start: 0.8501 (p90) cc_final: 0.8065 (p90) REVERT: l 17 GLU cc_start: 0.7919 (mp0) cc_final: 0.7494 (mp0) REVERT: l 90 THR cc_start: 0.8741 (m) cc_final: 0.8303 (p) REVERT: l 94 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7537 (tt) REVERT: l 99 PHE cc_start: 0.7325 (m-80) cc_final: 0.6730 (m-80) outliers start: 41 outliers final: 31 residues processed: 267 average time/residue: 0.1375 time to fit residues: 53.9006 Evaluate side-chains 277 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain a residue 423 GLN Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 68 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 113 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 50 optimal weight: 0.0570 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.103800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.080922 restraints weight = 37107.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084288 restraints weight = 19052.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086503 restraints weight = 13053.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087961 restraints weight = 10356.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.088920 restraints weight = 8899.361| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15642 Z= 0.131 Angle : 0.714 10.268 21390 Z= 0.335 Chirality : 0.041 0.171 2604 Planarity : 0.004 0.050 2514 Dihedral : 4.954 22.105 1902 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.14 % Favored : 94.69 % Rotamer: Outliers : 2.40 % Allowed : 17.02 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.34 (0.21), residues: 1731 helix: 1.32 (0.29), residues: 375 sheet: 0.09 (0.25), residues: 423 loop : -1.03 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 67 TYR 0.020 0.001 TYR a 419 PHE 0.025 0.001 PHE J 30 TRP 0.036 0.001 TRP H 52 HIS 0.005 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15516) covalent geometry : angle 0.67028 / 0.33 (21039) SS BOND : bond 0.00626 / 0.39 ( 27) SS BOND : angle 1.70111 / 1.04 ( 54) hydrogen bonds : bond 0.03429 / 2.30 ( 552) hydrogen bonds : angle 4.98957 / 3.55 ( 1566) link_ALPHA1-2 : bond 0.00042 / 0.02 ( 3) link_ALPHA1-2 : angle 1.70276 / 0.95 ( 9) link_ALPHA1-3 : bond 0.01521 / 0.69 ( 12) link_ALPHA1-3 : angle 3.33770 / 2.01 ( 36) link_ALPHA1-6 : bond 0.00733 / 0.40 ( 6) link_ALPHA1-6 : angle 1.27005 / 0.73 ( 18) link_BETA1-4 : bond 0.00717 / 0.46 ( 45) link_BETA1-4 : angle 2.13472 / 1.36 ( 135) link_NAG-ASN : bond 0.00233 / 0.15 ( 33) link_NAG-ASN : angle 1.47036 / 0.93 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2615.13 seconds wall clock time: 46 minutes 23.48 seconds (2783.48 seconds total)