Starting phenix.real_space_refine on Fri Jun 13 18:51:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejh_28182/06_2025/8ejh_28182.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejh_28182/06_2025/8ejh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejh_28182/06_2025/8ejh_28182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejh_28182/06_2025/8ejh_28182.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejh_28182/06_2025/8ejh_28182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejh_28182/06_2025/8ejh_28182.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 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 dihedrals: 21 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 21 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 dihedrals: 6 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 dihedrals: 21 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.71, per 1000 atoms: 0.71 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: 5.73 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.34 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: 5.63 Time building geometry restraints manager: 6.49 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 - 21.81: 9943 21.81 - 43.62: 275 43.62 - 65.43: 51 65.43 - 87.24: 111 87.24 - 109.05: 78 Dihedral angle restraints: 10458 sinusoidal: 5352 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 10455 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: 0.02 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: 1.410 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.850 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 17.279 109.053 7107 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 TRP 0.075 0.010 TRP H 52 HIS 0.006 0.002 HIS H 113 PHE 0.027 0.006 PHE l 99 TYR 0.048 0.007 TYR B 253 ARG 0.006 0.001 ARG h 75 Details of bonding type rmsd link_NAG-ASN : bond 0.07388 ( 33) link_NAG-ASN : angle 3.11118 ( 99) link_ALPHA1-6 : bond 0.04013 ( 6) link_ALPHA1-6 : angle 2.04702 ( 18) link_BETA1-4 : bond 0.07223 ( 45) link_BETA1-4 : angle 5.48432 ( 135) link_ALPHA1-2 : bond 0.08703 ( 3) link_ALPHA1-2 : angle 5.58010 ( 9) link_ALPHA1-3 : bond 0.07270 ( 12) link_ALPHA1-3 : angle 6.47357 ( 36) hydrogen bonds : bond 0.18297 ( 552) hydrogen bonds : angle 7.48017 ( 1566) SS BOND : bond 0.02120 ( 27) SS BOND : angle 3.70606 ( 54) covalent geometry : bond 0.02127 (15516) covalent geometry : angle 1.82534 (21039) *********************** 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 : 1.730 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: 0.7889 (tpp) REVERT: B 80 MET cc_start: 0.8297 (mmm) cc_final: 0.7502 (mmt) REVERT: B 194 MET cc_start: 0.8366 (tpp) cc_final: 0.8142 (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: 0.7908 (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: 0.8400 (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: 0.7786 (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: 0.7703 (ttp80) REVERT: L 90 THR cc_start: 0.8425 (m) cc_final: 0.8116 (p) REVERT: L 99 PHE cc_start: 0.6940 (m-80) cc_final: 0.6722 (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: 0.7902 (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: 0.7511 (pp) REVERT: h 87 PHE cc_start: 0.8310 (p90) cc_final: 0.8094 (p90) REVERT: l 18 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7700 (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: 0.3209 time to fit residues: 241.7181 Evaluate side-chains 284 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 0.0170 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 302 ASN b 302 ASN a 302 ASN ** a 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 GLN J 68 ASN K 6 GLN K 105 GLN l 6 GLN l 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.109531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084923 restraints weight = 36891.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088527 restraints weight = 19890.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090932 restraints weight = 13785.735| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15642 Z= 0.191 Angle : 0.920 10.038 21390 Z= 0.438 Chirality : 0.049 0.296 2604 Planarity : 0.005 0.044 2514 Dihedral : 14.596 74.792 3903 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.82 % Allowed : 10.27 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1731 helix: 0.41 (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 TRP 0.038 0.002 TRP h 52 HIS 0.010 0.002 HIS a 305 PHE 0.021 0.002 PHE H 30 TYR 0.023 0.002 TYR a 419 ARG 0.008 0.001 ARG b 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 33) link_NAG-ASN : angle 2.70375 ( 99) link_ALPHA1-6 : bond 0.00909 ( 6) link_ALPHA1-6 : angle 1.60042 ( 18) link_BETA1-4 : bond 0.01172 ( 45) link_BETA1-4 : angle 3.91878 ( 135) link_ALPHA1-2 : bond 0.00648 ( 3) link_ALPHA1-2 : angle 2.36354 ( 9) link_ALPHA1-3 : bond 0.02302 ( 12) link_ALPHA1-3 : angle 3.99718 ( 36) hydrogen bonds : bond 0.05580 ( 552) hydrogen bonds : angle 5.64934 ( 1566) SS BOND : bond 0.00540 ( 27) SS BOND : angle 1.41594 ( 54) covalent geometry : bond 0.00400 (15516) covalent geometry : angle 0.83105 (21039) *********************** 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 390 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 362 time to evaluate : 1.775 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: C 96 MET cc_start: 0.7775 (mmm) cc_final: 0.7470 (mmm) REVERT: C 161 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8156 (ttpp) REVERT: C 194 MET cc_start: 0.9112 (tpp) cc_final: 0.8320 (tpp) REVERT: B 116 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8520 (mmmt) REVERT: B 161 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7640 (tptt) REVERT: c 282 ARG cc_start: 0.8429 (tpt90) cc_final: 0.7878 (tpm170) REVERT: c 284 MET cc_start: 0.8310 (mtm) cc_final: 0.8074 (mtm) REVERT: c 303 GLU cc_start: 0.6085 (tp30) cc_final: 0.5534 (tp30) REVERT: c 351 MET cc_start: 0.8827 (tpp) cc_final: 0.8576 (tpp) REVERT: c 419 TYR cc_start: 0.7579 (t80) cc_final: 0.7330 (t80) REVERT: c 420 MET cc_start: 0.7346 (mmt) cc_final: 0.6267 (tpt) REVERT: A 96 MET cc_start: 0.7800 (mmm) cc_final: 0.7393 (mmm) REVERT: A 116 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8375 (mmmt) REVERT: A 134 MET cc_start: 0.9422 (tpp) cc_final: 0.9080 (tpp) REVERT: A 156 ASP cc_start: 0.8054 (p0) cc_final: 0.7758 (p0) REVERT: b 284 MET cc_start: 0.8236 (mtm) cc_final: 0.7613 (mtm) REVERT: b 303 GLU cc_start: 0.6222 (tp30) cc_final: 0.5768 (tp30) REVERT: b 305 HIS cc_start: 0.7323 (m90) cc_final: 0.6882 (m-70) REVERT: b 332 MET cc_start: 0.7518 (mmp) cc_final: 0.7281 (mmm) REVERT: b 420 MET cc_start: 0.7354 (mmt) cc_final: 0.6914 (tpt) REVERT: b 423 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7791 (mp10) REVERT: a 282 ARG cc_start: 0.8219 (tpt90) cc_final: 0.7933 (tpm170) REVERT: a 284 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8010 (mtp) REVERT: a 306 ASP cc_start: 0.8426 (p0) cc_final: 0.8173 (p0) REVERT: a 326 LEU cc_start: 0.7887 (mt) cc_final: 0.7615 (mp) REVERT: a 359 MET cc_start: 0.9029 (mtp) cc_final: 0.8762 (mtm) REVERT: a 409 ASN cc_start: 0.8823 (m-40) cc_final: 0.8413 (m110) REVERT: a 420 MET cc_start: 0.7451 (mmt) cc_final: 0.6888 (tpt) REVERT: H 6 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6415 (mm-30) REVERT: H 13 LEU cc_start: 0.7272 (mt) cc_final: 0.7049 (pp) REVERT: H 43 ARG cc_start: 0.8395 (ttp-170) cc_final: 0.8177 (ttp80) REVERT: H 51 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7006 (tt0) REVERT: H 78 ILE cc_start: 0.8425 (mt) cc_final: 0.8142 (tp) REVERT: H 98 ASP cc_start: 0.7242 (m-30) cc_final: 0.6829 (m-30) REVERT: H 112 TYR cc_start: 0.7883 (p90) cc_final: 0.7154 (p90) REVERT: L 17 GLU cc_start: 0.6749 (mp0) cc_final: 0.6462 (mp0) REVERT: L 18 ARG cc_start: 0.8330 (ttm170) cc_final: 0.7781 (ttp80) REVERT: L 90 THR cc_start: 0.8213 (m) cc_final: 0.7791 (p) REVERT: L 94 LEU cc_start: 0.7674 (tp) cc_final: 0.6943 (tt) REVERT: L 99 PHE cc_start: 0.6697 (m-80) cc_final: 0.5665 (m-80) REVERT: L 125 GLU cc_start: 0.6705 (tt0) cc_final: 0.6352 (tt0) REVERT: J 43 ARG cc_start: 0.8102 (ttp-170) cc_final: 0.7832 (ttp-170) REVERT: J 52 TRP cc_start: 0.7701 (t60) cc_final: 0.7417 (t60) REVERT: J 98 ASP cc_start: 0.6940 (m-30) cc_final: 0.6540 (m-30) REVERT: J 122 THR cc_start: 0.7038 (m) cc_final: 0.6793 (p) REVERT: K 5 THR cc_start: 0.7927 (m) cc_final: 0.7706 (p) REVERT: K 18 ARG cc_start: 0.8380 (ttm170) cc_final: 0.7725 (ttp80) REVERT: K 90 THR cc_start: 0.8071 (m) cc_final: 0.7789 (p) REVERT: K 94 LEU cc_start: 0.7780 (tp) cc_final: 0.7328 (tt) REVERT: K 99 PHE cc_start: 0.6940 (m-80) cc_final: 0.6370 (m-80) REVERT: h 43 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7860 (ttp80) REVERT: h 53 ILE cc_start: 0.8143 (mt) cc_final: 0.7844 (mt) REVERT: h 78 ILE cc_start: 0.8352 (mt) cc_final: 0.7776 (tp) REVERT: h 87 PHE cc_start: 0.8487 (p90) cc_final: 0.7888 (p90) REVERT: h 112 TYR cc_start: 0.8160 (p90) cc_final: 0.7807 (p90) REVERT: l 17 GLU cc_start: 0.7407 (mp0) cc_final: 0.6988 (mp0) REVERT: l 18 ARG cc_start: 0.8617 (ttm170) cc_final: 0.7812 (ttp80) REVERT: l 90 THR cc_start: 0.8135 (m) cc_final: 0.7744 (p) REVERT: l 98 ASP cc_start: 0.8411 (m-30) cc_final: 0.8196 (m-30) outliers start: 28 outliers final: 18 residues processed: 375 average time/residue: 0.2980 time to fit residues: 161.2813 Evaluate side-chains 308 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 289 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 273 ASP 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 158 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 423 GLN L 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.105083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.081856 restraints weight = 36469.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085229 restraints weight = 18838.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087504 restraints weight = 12927.377| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15642 Z= 0.206 Angle : 0.846 12.165 21390 Z= 0.396 Chirality : 0.047 0.242 2604 Planarity : 0.004 0.037 2514 Dihedral : 10.566 62.783 3903 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.31 % Allowed : 11.76 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1731 helix: 0.73 (0.28), residues: 375 sheet: 0.17 (0.25), residues: 420 loop : -0.66 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 210 HIS 0.007 0.002 HIS B 230 PHE 0.032 0.002 PHE J 87 TYR 0.021 0.002 TYR a 419 ARG 0.004 0.001 ARG b 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 33) link_NAG-ASN : angle 2.12078 ( 99) link_ALPHA1-6 : bond 0.00491 ( 6) link_ALPHA1-6 : angle 1.74442 ( 18) link_BETA1-4 : bond 0.00994 ( 45) link_BETA1-4 : angle 3.16528 ( 135) link_ALPHA1-2 : bond 0.00145 ( 3) link_ALPHA1-2 : angle 1.91199 ( 9) link_ALPHA1-3 : bond 0.01993 ( 12) link_ALPHA1-3 : angle 3.56350 ( 36) hydrogen bonds : bond 0.04663 ( 552) hydrogen bonds : angle 5.41690 ( 1566) SS BOND : bond 0.00623 ( 27) SS BOND : angle 1.88012 ( 54) covalent geometry : bond 0.00448 (15516) covalent geometry : angle 0.77928 (21039) *********************** 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 363 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 312 time to evaluate : 1.652 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: C 72 GLU cc_start: 0.7426 (pm20) cc_final: 0.7160 (pm20) REVERT: C 96 MET cc_start: 0.7877 (mmm) cc_final: 0.7634 (mmm) REVERT: C 156 ASP cc_start: 0.7651 (t70) cc_final: 0.6587 (t0) REVERT: C 161 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8257 (ttpp) REVERT: C 228 GLU cc_start: 0.8256 (mp0) cc_final: 0.8048 (mp0) REVERT: B 116 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8773 (mmmt) REVERT: B 156 ASP cc_start: 0.7906 (t70) cc_final: 0.7664 (t0) REVERT: B 161 LYS cc_start: 0.8581 (ttmt) cc_final: 0.7890 (tptt) REVERT: c 282 ARG cc_start: 0.8574 (tpt90) cc_final: 0.7936 (tpm170) REVERT: c 303 GLU cc_start: 0.6323 (tp30) cc_final: 0.5279 (tp30) REVERT: c 326 LEU cc_start: 0.7971 (mp) cc_final: 0.7491 (tp) REVERT: c 351 MET cc_start: 0.8888 (tpp) cc_final: 0.8612 (tpp) REVERT: c 419 TYR cc_start: 0.7542 (t80) cc_final: 0.7330 (t80) REVERT: c 420 MET cc_start: 0.7400 (mmt) cc_final: 0.6434 (tpt) REVERT: A 96 MET cc_start: 0.7926 (mmm) cc_final: 0.7720 (mmm) REVERT: A 104 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: A 116 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8725 (mmmt) REVERT: A 156 ASP cc_start: 0.8001 (p0) cc_final: 0.7738 (p0) REVERT: A 161 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8388 (ttpp) REVERT: A 194 MET cc_start: 0.8891 (tpp) cc_final: 0.8650 (tpp) REVERT: A 245 LEU cc_start: 0.8566 (tp) cc_final: 0.8257 (tp) REVERT: b 284 MET cc_start: 0.8213 (mtm) cc_final: 0.7748 (mtm) REVERT: b 303 GLU cc_start: 0.6564 (tp30) cc_final: 0.6312 (tp30) REVERT: b 418 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8464 (mt-10) REVERT: b 419 TYR cc_start: 0.6779 (t80) cc_final: 0.6010 (t80) REVERT: b 420 MET cc_start: 0.7721 (mmt) cc_final: 0.6907 (tpt) REVERT: a 284 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8100 (mtp) REVERT: a 303 GLU cc_start: 0.6343 (tp30) cc_final: 0.6039 (tp30) REVERT: a 306 ASP cc_start: 0.8230 (p0) cc_final: 0.8003 (p0) REVERT: a 348 GLN cc_start: 0.5141 (mt0) cc_final: 0.4303 (tt0) REVERT: a 409 ASN cc_start: 0.8701 (m-40) cc_final: 0.8354 (m110) REVERT: a 420 MET cc_start: 0.7901 (mmt) cc_final: 0.7353 (tpt) REVERT: H 13 LEU cc_start: 0.7438 (mt) cc_final: 0.7182 (pp) REVERT: H 53 ILE cc_start: 0.8257 (mt) cc_final: 0.7879 (mt) REVERT: H 98 ASP cc_start: 0.7432 (m-30) cc_final: 0.7009 (m-30) REVERT: H 110 TYR cc_start: 0.8396 (t80) cc_final: 0.7922 (t80) REVERT: H 112 TYR cc_start: 0.8212 (p90) cc_final: 0.7302 (p90) REVERT: L 17 GLU cc_start: 0.7163 (mp0) cc_final: 0.6853 (mp0) REVERT: L 18 ARG cc_start: 0.8385 (ttm170) cc_final: 0.7641 (ttp80) REVERT: L 90 THR cc_start: 0.8398 (m) cc_final: 0.8054 (p) REVERT: L 94 LEU cc_start: 0.7849 (tp) cc_final: 0.7147 (tt) REVERT: L 99 PHE cc_start: 0.7187 (m-80) cc_final: 0.6310 (m-80) REVERT: L 122 THR cc_start: 0.8012 (p) cc_final: 0.7774 (p) REVERT: J 5 GLN cc_start: 0.7213 (tp40) cc_final: 0.6760 (tp-100) REVERT: J 19 LEU cc_start: 0.8558 (tp) cc_final: 0.8327 (tt) REVERT: J 52 TRP cc_start: 0.7973 (t60) cc_final: 0.7337 (t60) REVERT: J 98 ASP cc_start: 0.7165 (m-30) cc_final: 0.6694 (m-30) REVERT: K 5 THR cc_start: 0.7794 (m) cc_final: 0.7590 (p) REVERT: K 17 GLU cc_start: 0.7542 (mp0) cc_final: 0.7193 (mp0) REVERT: K 90 THR cc_start: 0.8383 (m) cc_final: 0.8088 (p) REVERT: K 94 LEU cc_start: 0.7732 (tp) cc_final: 0.7395 (tt) REVERT: K 99 PHE cc_start: 0.7335 (m-80) cc_final: 0.6776 (m-80) REVERT: h 43 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8063 (mtm110) REVERT: h 52 TRP cc_start: 0.7994 (t60) cc_final: 0.7680 (t60) REVERT: h 53 ILE cc_start: 0.8293 (mt) cc_final: 0.7779 (mt) REVERT: h 87 PHE cc_start: 0.8396 (p90) cc_final: 0.8153 (p90) REVERT: h 112 TYR cc_start: 0.8135 (p90) cc_final: 0.7473 (p90) REVERT: l 17 GLU cc_start: 0.7677 (mp0) cc_final: 0.7344 (mp0) REVERT: l 18 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7615 (ttp80) REVERT: l 90 THR cc_start: 0.8350 (m) cc_final: 0.7946 (p) REVERT: l 94 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7538 (tt) REVERT: l 99 PHE cc_start: 0.7226 (m-80) cc_final: 0.6448 (m-80) outliers start: 51 outliers final: 30 residues processed: 334 average time/residue: 0.2975 time to fit residues: 144.8176 Evaluate side-chains 308 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP 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 292 CYS 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 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 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 323 ILE Chi-restraints excluded: chain a residue 388 VAL 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 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 39 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 130 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 141 optimal weight: 0.0970 chunk 25 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS K 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.106730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082707 restraints weight = 37280.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.086189 restraints weight = 19972.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.088493 restraints weight = 13930.835| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15642 Z= 0.149 Angle : 0.760 11.088 21390 Z= 0.356 Chirality : 0.044 0.260 2604 Planarity : 0.004 0.035 2514 Dihedral : 8.268 50.477 3903 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.38 % Allowed : 12.80 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1731 helix: 1.00 (0.28), residues: 375 sheet: 0.22 (0.25), residues: 417 loop : -0.71 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP H 52 HIS 0.005 0.001 HIS B 230 PHE 0.012 0.001 PHE H 30 TYR 0.019 0.001 TYR a 419 ARG 0.004 0.000 ARG b 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 33) link_NAG-ASN : angle 1.86213 ( 99) link_ALPHA1-6 : bond 0.00787 ( 6) link_ALPHA1-6 : angle 1.66133 ( 18) link_BETA1-4 : bond 0.00853 ( 45) link_BETA1-4 : angle 2.78617 ( 135) link_ALPHA1-2 : bond 0.00075 ( 3) link_ALPHA1-2 : angle 1.94048 ( 9) link_ALPHA1-3 : bond 0.01803 ( 12) link_ALPHA1-3 : angle 3.22602 ( 36) hydrogen bonds : bond 0.03929 ( 552) hydrogen bonds : angle 5.20742 ( 1566) SS BOND : bond 0.00532 ( 27) SS BOND : angle 2.17147 ( 54) covalent geometry : bond 0.00326 (15516) covalent geometry : angle 0.69790 (21039) *********************** 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 368 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 316 time to evaluate : 2.501 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: C 67 GLU cc_start: 0.7577 (tt0) cc_final: 0.7356 (tm-30) REVERT: C 96 MET cc_start: 0.7762 (mmm) cc_final: 0.7562 (mmm) REVERT: C 116 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8770 (mmmt) REVERT: C 156 ASP cc_start: 0.7822 (t70) cc_final: 0.6737 (t0) REVERT: C 161 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8229 (ttpp) REVERT: C 194 MET cc_start: 0.9092 (tpp) cc_final: 0.8267 (tpp) REVERT: C 244 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7979 (tp) REVERT: B 116 LYS cc_start: 0.9107 (mmtm) cc_final: 0.8818 (mmmt) REVERT: B 156 ASP cc_start: 0.7924 (t70) cc_final: 0.7464 (t0) REVERT: B 161 LYS cc_start: 0.8526 (ttmt) cc_final: 0.7848 (tptt) REVERT: c 282 ARG cc_start: 0.8473 (tpt90) cc_final: 0.7847 (tpm170) REVERT: c 303 GLU cc_start: 0.5926 (tp30) cc_final: 0.5211 (tp30) REVERT: c 326 LEU cc_start: 0.7999 (mp) cc_final: 0.7524 (tp) REVERT: c 420 MET cc_start: 0.7497 (mmt) cc_final: 0.6563 (tpt) REVERT: A 80 MET cc_start: 0.8738 (mmt) cc_final: 0.8111 (mmm) REVERT: A 96 MET cc_start: 0.7886 (mmm) cc_final: 0.7659 (mmm) REVERT: A 116 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8788 (mmmt) REVERT: A 156 ASP cc_start: 0.8086 (p0) cc_final: 0.7787 (p0) REVERT: A 161 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8022 (tptt) REVERT: b 284 MET cc_start: 0.8187 (mtm) cc_final: 0.7618 (mtm) REVERT: b 303 GLU cc_start: 0.7033 (tp30) cc_final: 0.6831 (tp30) REVERT: b 311 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8287 (t0) REVERT: b 332 MET cc_start: 0.7828 (tpp) cc_final: 0.7526 (tpp) REVERT: b 351 MET cc_start: 0.8898 (tpp) cc_final: 0.8688 (mmm) REVERT: b 420 MET cc_start: 0.7739 (mmt) cc_final: 0.7332 (tpt) REVERT: a 284 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7983 (mtp) REVERT: a 303 GLU cc_start: 0.6876 (tp30) cc_final: 0.6429 (tp30) REVERT: a 311 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7899 (t0) REVERT: a 326 LEU cc_start: 0.7856 (mt) cc_final: 0.7153 (mt) REVERT: a 332 MET cc_start: 0.7719 (tpp) cc_final: 0.7442 (tpp) REVERT: a 348 GLN cc_start: 0.5049 (mt0) cc_final: 0.4276 (tt0) REVERT: a 420 MET cc_start: 0.8047 (mmt) cc_final: 0.7499 (tpt) REVERT: H 53 ILE cc_start: 0.8312 (mt) cc_final: 0.7795 (mt) REVERT: H 90 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8138 (mtpp) REVERT: H 98 ASP cc_start: 0.7307 (m-30) cc_final: 0.6911 (m-30) REVERT: H 110 TYR cc_start: 0.8288 (t80) cc_final: 0.8027 (t80) REVERT: H 112 TYR cc_start: 0.7994 (p90) cc_final: 0.7121 (p90) REVERT: L 17 GLU cc_start: 0.7206 (mp0) cc_final: 0.6920 (mp0) REVERT: L 18 ARG cc_start: 0.8388 (ttm170) cc_final: 0.7641 (ttp80) REVERT: L 90 THR cc_start: 0.8379 (m) cc_final: 0.8140 (p) REVERT: L 94 LEU cc_start: 0.7809 (tp) cc_final: 0.7111 (tt) REVERT: L 99 PHE cc_start: 0.7113 (m-80) cc_final: 0.6273 (m-80) REVERT: J 5 GLN cc_start: 0.7247 (tp40) cc_final: 0.6825 (tp-100) REVERT: J 43 ARG cc_start: 0.8423 (ttp-170) cc_final: 0.8001 (mtm110) REVERT: J 52 TRP cc_start: 0.7997 (t60) cc_final: 0.7293 (t60) REVERT: J 98 ASP cc_start: 0.6983 (m-30) cc_final: 0.6475 (m-30) REVERT: K 5 THR cc_start: 0.7885 (m) cc_final: 0.7607 (p) REVERT: K 17 GLU cc_start: 0.7642 (mp0) cc_final: 0.6743 (mp0) REVERT: K 90 THR cc_start: 0.8517 (m) cc_final: 0.8238 (p) REVERT: K 94 LEU cc_start: 0.7658 (tp) cc_final: 0.7271 (tt) REVERT: K 99 PHE cc_start: 0.7374 (m-80) cc_final: 0.6796 (m-80) REVERT: h 13 LEU cc_start: 0.7063 (mt) cc_final: 0.6847 (pp) REVERT: h 43 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7992 (mtm110) REVERT: h 52 TRP cc_start: 0.7988 (t60) cc_final: 0.7613 (t60) REVERT: h 53 ILE cc_start: 0.8298 (mt) cc_final: 0.7755 (mt) REVERT: h 87 PHE cc_start: 0.8321 (p90) cc_final: 0.7882 (p90) REVERT: l 17 GLU cc_start: 0.7733 (mp0) cc_final: 0.7407 (mp0) REVERT: l 90 THR cc_start: 0.8473 (m) cc_final: 0.8129 (p) REVERT: l 94 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7392 (tt) REVERT: l 99 PHE cc_start: 0.7174 (m-80) cc_final: 0.6613 (m-80) outliers start: 52 outliers final: 30 residues processed: 346 average time/residue: 0.2902 time to fit residues: 147.3186 Evaluate side-chains 309 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP 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 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 21 LEU Chi-restraints excluded: chain H residue 90 LYS 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 L residue 117 THR 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 39 LEU Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 73 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.104520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.080386 restraints weight = 38436.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083700 restraints weight = 20521.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.085908 restraints weight = 14471.587| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15642 Z= 0.192 Angle : 0.764 10.851 21390 Z= 0.361 Chirality : 0.045 0.263 2604 Planarity : 0.004 0.039 2514 Dihedral : 7.496 57.473 3903 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.38 % Allowed : 13.58 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1731 helix: 1.10 (0.28), residues: 375 sheet: 0.22 (0.25), residues: 423 loop : -0.86 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 52 HIS 0.005 0.001 HIS A 141 PHE 0.019 0.002 PHE J 87 TYR 0.023 0.002 TYR a 419 ARG 0.006 0.001 ARG a 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 33) link_NAG-ASN : angle 1.86377 ( 99) link_ALPHA1-6 : bond 0.00839 ( 6) link_ALPHA1-6 : angle 1.62389 ( 18) link_BETA1-4 : bond 0.00770 ( 45) link_BETA1-4 : angle 2.59777 ( 135) link_ALPHA1-2 : bond 0.00030 ( 3) link_ALPHA1-2 : angle 1.97375 ( 9) link_ALPHA1-3 : bond 0.01741 ( 12) link_ALPHA1-3 : angle 3.32633 ( 36) hydrogen bonds : bond 0.04078 ( 552) hydrogen bonds : angle 5.15794 ( 1566) SS BOND : bond 0.00884 ( 27) SS BOND : angle 2.09561 ( 54) covalent geometry : bond 0.00433 (15516) covalent geometry : angle 0.70719 (21039) *********************** 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 338 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 286 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7263 (pm20) cc_final: 0.6857 (mp0) REVERT: C 116 LYS cc_start: 0.9149 (mmtm) cc_final: 0.8809 (mmmt) REVERT: C 156 ASP cc_start: 0.8037 (t70) cc_final: 0.6956 (t0) REVERT: C 161 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8283 (ttpp) REVERT: C 214 MET cc_start: 0.8025 (ptp) cc_final: 0.7678 (ptp) REVERT: B 116 LYS cc_start: 0.9181 (mmtm) cc_final: 0.8894 (mmmt) REVERT: B 153 MET cc_start: 0.9029 (ttt) cc_final: 0.8727 (ttm) REVERT: B 156 ASP cc_start: 0.8015 (t70) cc_final: 0.7682 (t0) REVERT: B 161 LYS cc_start: 0.8598 (ttmt) cc_final: 0.7957 (tptt) REVERT: c 282 ARG cc_start: 0.8584 (tpt90) cc_final: 0.7956 (tpm170) REVERT: c 303 GLU cc_start: 0.6304 (tp30) cc_final: 0.5795 (tp30) REVERT: c 311 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7972 (t0) REVERT: c 312 MET cc_start: 0.8970 (mmp) cc_final: 0.8767 (mmm) REVERT: c 326 LEU cc_start: 0.8220 (mp) cc_final: 0.8010 (mp) REVERT: c 420 MET cc_start: 0.7390 (mmt) cc_final: 0.6489 (tpt) REVERT: A 67 GLU cc_start: 0.7499 (tt0) cc_final: 0.7070 (tm-30) REVERT: A 116 LYS cc_start: 0.9134 (mmtm) cc_final: 0.8876 (mmmt) REVERT: A 156 ASP cc_start: 0.8011 (p0) cc_final: 0.7441 (p0) REVERT: A 161 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8164 (ttpp) REVERT: b 284 MET cc_start: 0.8204 (mtm) cc_final: 0.7679 (mtm) REVERT: b 303 GLU cc_start: 0.7232 (tp30) cc_final: 0.6812 (tp30) REVERT: b 311 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8241 (t70) REVERT: b 420 MET cc_start: 0.7773 (mmt) cc_final: 0.7114 (tpt) REVERT: a 282 ARG cc_start: 0.8428 (tpt90) cc_final: 0.7842 (tpm170) REVERT: a 284 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8000 (mtp) REVERT: a 303 GLU cc_start: 0.7041 (tp30) cc_final: 0.6647 (tp30) REVERT: a 311 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7551 (t0) REVERT: a 348 GLN cc_start: 0.4943 (mt0) cc_final: 0.4179 (tt0) REVERT: a 410 MET cc_start: 0.7960 (mtp) cc_final: 0.7606 (ttm) REVERT: a 419 TYR cc_start: 0.6158 (OUTLIER) cc_final: 0.5306 (t80) REVERT: a 420 MET cc_start: 0.7960 (mmt) cc_final: 0.7223 (tpt) REVERT: H 5 GLN cc_start: 0.7192 (tp40) cc_final: 0.6780 (tp-100) REVERT: H 90 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8147 (mtpp) REVERT: H 98 ASP cc_start: 0.7424 (m-30) cc_final: 0.7043 (m-30) REVERT: L 17 GLU cc_start: 0.7353 (mp0) cc_final: 0.7017 (mp0) REVERT: L 18 ARG cc_start: 0.8406 (ttm170) cc_final: 0.7558 (ttp80) REVERT: L 90 THR cc_start: 0.8579 (m) cc_final: 0.8373 (p) REVERT: L 94 LEU cc_start: 0.7782 (tp) cc_final: 0.7106 (tt) REVERT: L 99 PHE cc_start: 0.7297 (m-80) cc_final: 0.6480 (m-80) REVERT: J 5 GLN cc_start: 0.7159 (tp40) cc_final: 0.6809 (tp-100) REVERT: J 43 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.8043 (mtm110) REVERT: J 52 TRP cc_start: 0.7978 (t60) cc_final: 0.7290 (t60) REVERT: J 98 ASP cc_start: 0.6993 (m-30) cc_final: 0.6641 (m-30) REVERT: K 5 THR cc_start: 0.7740 (m) cc_final: 0.7508 (p) REVERT: K 17 GLU cc_start: 0.7828 (mp0) cc_final: 0.6869 (mp0) REVERT: K 90 THR cc_start: 0.8702 (m) cc_final: 0.8442 (p) REVERT: K 94 LEU cc_start: 0.7672 (tp) cc_final: 0.7214 (tt) REVERT: K 99 PHE cc_start: 0.7672 (m-80) cc_final: 0.6964 (m-80) REVERT: h 43 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7985 (mtm110) REVERT: h 53 ILE cc_start: 0.8380 (mt) cc_final: 0.7874 (mt) REVERT: h 87 PHE cc_start: 0.8433 (p90) cc_final: 0.7897 (p90) REVERT: l 17 GLU cc_start: 0.7774 (mp0) cc_final: 0.7428 (mp0) REVERT: l 90 THR cc_start: 0.8607 (m) cc_final: 0.8267 (p) REVERT: l 94 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7478 (tt) REVERT: l 99 PHE cc_start: 0.7320 (m-80) cc_final: 0.6567 (m-80) outliers start: 52 outliers final: 35 residues processed: 315 average time/residue: 0.3749 time to fit residues: 173.2535 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 : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP 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 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 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain b residue 287 GLU 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 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 419 TYR Chi-restraints excluded: chain a residue 423 GLN Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 90 LYS 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 L residue 117 THR Chi-restraints excluded: chain L residue 124 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 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 5 THR Chi-restraints excluded: chain l residue 39 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 166 optimal weight: 0.0670 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.107926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083479 restraints weight = 37361.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.086749 restraints weight = 20522.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088877 restraints weight = 14770.397| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15642 Z= 0.161 Angle : 0.738 10.177 21390 Z= 0.348 Chirality : 0.044 0.264 2604 Planarity : 0.004 0.046 2514 Dihedral : 7.132 58.485 3903 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.77 % Allowed : 13.78 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1731 helix: 1.19 (0.28), residues: 375 sheet: 0.16 (0.25), residues: 426 loop : -0.88 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP H 52 HIS 0.009 0.001 HIS c 305 PHE 0.021 0.001 PHE J 87 TYR 0.019 0.001 TYR a 419 ARG 0.003 0.000 ARG K 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 33) link_NAG-ASN : angle 1.71753 ( 99) link_ALPHA1-6 : bond 0.00955 ( 6) link_ALPHA1-6 : angle 1.58687 ( 18) link_BETA1-4 : bond 0.00782 ( 45) link_BETA1-4 : angle 2.48073 ( 135) link_ALPHA1-2 : bond 0.00058 ( 3) link_ALPHA1-2 : angle 2.05615 ( 9) link_ALPHA1-3 : bond 0.01617 ( 12) link_ALPHA1-3 : angle 3.28549 ( 36) hydrogen bonds : bond 0.03760 ( 552) hydrogen bonds : angle 5.11154 ( 1566) SS BOND : bond 0.00763 ( 27) SS BOND : angle 1.98641 ( 54) covalent geometry : bond 0.00358 (15516) covalent geometry : angle 0.68395 (21039) *********************** 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 342 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7302 (pm20) cc_final: 0.6930 (pm20) REVERT: C 116 LYS cc_start: 0.9147 (mmtm) cc_final: 0.8842 (mmmt) REVERT: C 156 ASP cc_start: 0.7959 (t70) cc_final: 0.6869 (t0) REVERT: C 161 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8301 (ttpp) REVERT: C 194 MET cc_start: 0.8861 (tpp) cc_final: 0.8382 (ttp) REVERT: C 214 MET cc_start: 0.7940 (ptp) cc_final: 0.7676 (ptp) REVERT: B 116 LYS cc_start: 0.9191 (mmtm) cc_final: 0.8938 (mmmt) REVERT: B 151 GLU cc_start: 0.8239 (pm20) cc_final: 0.7962 (pm20) REVERT: B 156 ASP cc_start: 0.8056 (t70) cc_final: 0.7691 (t0) REVERT: B 161 LYS cc_start: 0.8587 (ttmt) cc_final: 0.7961 (tptt) REVERT: c 282 ARG cc_start: 0.8566 (tpt90) cc_final: 0.7984 (tpm170) REVERT: c 311 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7979 (t0) REVERT: c 348 GLN cc_start: 0.4877 (mt0) cc_final: 0.4180 (tt0) REVERT: c 420 MET cc_start: 0.7501 (mmt) cc_final: 0.6626 (tpt) REVERT: A 67 GLU cc_start: 0.7677 (tt0) cc_final: 0.7439 (tm-30) REVERT: A 116 LYS cc_start: 0.9153 (mmtm) cc_final: 0.8918 (mmmt) REVERT: A 151 GLU cc_start: 0.8300 (pm20) cc_final: 0.8079 (pm20) REVERT: A 161 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8464 (ttpp) REVERT: b 303 GLU cc_start: 0.7237 (tp30) cc_final: 0.6911 (tp30) REVERT: b 326 LEU cc_start: 0.8347 (mp) cc_final: 0.7876 (tp) REVERT: b 332 MET cc_start: 0.7819 (tpp) cc_final: 0.7279 (tpp) REVERT: b 420 MET cc_start: 0.7681 (mmt) cc_final: 0.7029 (tpt) REVERT: a 282 ARG cc_start: 0.8415 (tpt90) cc_final: 0.7851 (tpm170) REVERT: a 284 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8234 (mtp) REVERT: a 303 GLU cc_start: 0.7107 (tp30) cc_final: 0.6513 (tp30) REVERT: a 311 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7902 (t0) REVERT: a 326 LEU cc_start: 0.8120 (mt) cc_final: 0.7718 (mp) REVERT: a 332 MET cc_start: 0.7942 (tpp) cc_final: 0.7256 (tpp) REVERT: a 348 GLN cc_start: 0.5217 (mt0) cc_final: 0.4243 (tt0) REVERT: a 410 MET cc_start: 0.8049 (mtp) cc_final: 0.7635 (ttm) REVERT: a 419 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5163 (t80) REVERT: a 420 MET cc_start: 0.7993 (mmt) cc_final: 0.7283 (tpt) REVERT: H 5 GLN cc_start: 0.7356 (tp40) cc_final: 0.7011 (tp-100) REVERT: H 6 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6921 (mm-30) REVERT: H 21 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7182 (mm) REVERT: H 51 GLU cc_start: 0.7441 (tt0) cc_final: 0.7231 (tt0) REVERT: H 53 ILE cc_start: 0.8506 (mt) cc_final: 0.8297 (mt) REVERT: H 90 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8231 (mtpp) REVERT: H 98 ASP cc_start: 0.7478 (m-30) cc_final: 0.7091 (m-30) REVERT: H 112 TYR cc_start: 0.8213 (p90) cc_final: 0.7311 (p90) REVERT: L 17 GLU cc_start: 0.7521 (mp0) cc_final: 0.7192 (mp0) REVERT: L 18 ARG cc_start: 0.8523 (ttm170) cc_final: 0.7582 (ttp80) REVERT: L 94 LEU cc_start: 0.7799 (tp) cc_final: 0.7151 (tt) REVERT: L 99 PHE cc_start: 0.7259 (m-80) cc_final: 0.6542 (m-80) REVERT: J 5 GLN cc_start: 0.7089 (tp40) cc_final: 0.6697 (tp-100) REVERT: J 30 PHE cc_start: 0.8287 (t80) cc_final: 0.8005 (t80) REVERT: J 43 ARG cc_start: 0.8504 (ttp-170) cc_final: 0.8194 (mtm110) REVERT: J 52 TRP cc_start: 0.8051 (t60) cc_final: 0.7662 (t60) REVERT: J 98 ASP cc_start: 0.7009 (m-30) cc_final: 0.6616 (m-30) REVERT: K 5 THR cc_start: 0.7796 (m) cc_final: 0.7591 (p) REVERT: K 17 GLU cc_start: 0.8138 (mp0) cc_final: 0.7255 (mp0) REVERT: K 42 TYR cc_start: 0.8681 (m-80) cc_final: 0.8016 (m-80) REVERT: K 90 THR cc_start: 0.8780 (m) cc_final: 0.8549 (p) REVERT: K 94 LEU cc_start: 0.7745 (tp) cc_final: 0.7321 (tt) REVERT: K 99 PHE cc_start: 0.7616 (m-80) cc_final: 0.6960 (m-80) REVERT: h 5 GLN cc_start: 0.6907 (tp40) cc_final: 0.6362 (tp-100) REVERT: h 43 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8157 (mtm110) REVERT: h 52 TRP cc_start: 0.8063 (t60) cc_final: 0.7618 (t60) REVERT: h 53 ILE cc_start: 0.8509 (mt) cc_final: 0.7934 (mt) REVERT: h 85 ASN cc_start: 0.7232 (p0) cc_final: 0.6984 (p0) REVERT: h 87 PHE cc_start: 0.8427 (p90) cc_final: 0.7999 (p90) REVERT: l 17 GLU cc_start: 0.7953 (mp0) cc_final: 0.7610 (mp0) REVERT: l 90 THR cc_start: 0.8720 (m) cc_final: 0.8398 (p) REVERT: l 94 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7531 (tt) REVERT: l 99 PHE cc_start: 0.7325 (m-80) cc_final: 0.6750 (m-80) outliers start: 58 outliers final: 34 residues processed: 315 average time/residue: 0.3130 time to fit residues: 145.4946 Evaluate side-chains 293 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 214 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 411 ILE 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 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 419 TYR 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 25 VAL Chi-restraints excluded: chain H residue 90 LYS 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 5 THR Chi-restraints excluded: chain l residue 39 LEU Chi-restraints excluded: chain l residue 94 LEU 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 21 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.108839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.083289 restraints weight = 38271.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086670 restraints weight = 20829.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.088883 restraints weight = 14888.830| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15642 Z= 0.142 Angle : 0.715 10.444 21390 Z= 0.336 Chirality : 0.043 0.257 2604 Planarity : 0.004 0.049 2514 Dihedral : 6.747 55.270 3903 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.57 % Allowed : 14.42 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1731 helix: 1.17 (0.29), residues: 375 sheet: 0.16 (0.25), residues: 426 loop : -0.93 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H 52 HIS 0.011 0.001 HIS c 305 PHE 0.023 0.001 PHE J 87 TYR 0.019 0.001 TYR a 419 ARG 0.012 0.000 ARG l 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 33) link_NAG-ASN : angle 1.60709 ( 99) link_ALPHA1-6 : bond 0.01033 ( 6) link_ALPHA1-6 : angle 1.52709 ( 18) link_BETA1-4 : bond 0.00775 ( 45) link_BETA1-4 : angle 2.37772 ( 135) link_ALPHA1-2 : bond 0.00076 ( 3) link_ALPHA1-2 : angle 2.07250 ( 9) link_ALPHA1-3 : bond 0.01564 ( 12) link_ALPHA1-3 : angle 3.25060 ( 36) hydrogen bonds : bond 0.03576 ( 552) hydrogen bonds : angle 5.02210 ( 1566) SS BOND : bond 0.00640 ( 27) SS BOND : angle 1.77236 ( 54) covalent geometry : bond 0.00312 (15516) covalent geometry : angle 0.66457 (21039) *********************** 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 331 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 276 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 MET cc_start: 0.8196 (mmm) cc_final: 0.7949 (mmm) REVERT: C 82 MET cc_start: 0.8673 (ptt) cc_final: 0.8244 (pmm) REVERT: C 116 LYS cc_start: 0.9144 (mmtm) cc_final: 0.8836 (mmmt) REVERT: C 156 ASP cc_start: 0.7932 (t70) cc_final: 0.6788 (t0) REVERT: C 161 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8274 (ttpp) REVERT: C 194 MET cc_start: 0.8905 (tpp) cc_final: 0.8426 (ttp) REVERT: C 214 MET cc_start: 0.7919 (ptp) cc_final: 0.7693 (ptp) REVERT: B 116 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8920 (mmmt) REVERT: B 156 ASP cc_start: 0.8032 (t70) cc_final: 0.7660 (t0) REVERT: B 161 LYS cc_start: 0.8559 (ttmt) cc_final: 0.7934 (tptt) REVERT: c 282 ARG cc_start: 0.8583 (tpt90) cc_final: 0.8020 (tpm170) REVERT: c 311 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7941 (t0) REVERT: c 326 LEU cc_start: 0.8291 (mp) cc_final: 0.7882 (tp) REVERT: c 348 GLN cc_start: 0.4785 (mt0) cc_final: 0.4061 (tt0) REVERT: c 420 MET cc_start: 0.7487 (mmt) cc_final: 0.6788 (tpt) REVERT: A 116 LYS cc_start: 0.9172 (mmtm) cc_final: 0.8953 (mmmt) REVERT: A 161 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8480 (ttpp) REVERT: A 194 MET cc_start: 0.8756 (tpp) cc_final: 0.8071 (ttm) REVERT: b 284 MET cc_start: 0.8347 (mtm) cc_final: 0.7650 (mtm) REVERT: b 303 GLU cc_start: 0.7308 (tp30) cc_final: 0.6924 (tp30) REVERT: b 326 LEU cc_start: 0.8486 (mp) cc_final: 0.8039 (tp) REVERT: b 332 MET cc_start: 0.7729 (tpp) cc_final: 0.7384 (tpp) REVERT: b 410 MET cc_start: 0.7977 (mmm) cc_final: 0.7631 (mmm) REVERT: b 420 MET cc_start: 0.7681 (mmt) cc_final: 0.7022 (tpt) REVERT: a 282 ARG cc_start: 0.8444 (tpt90) cc_final: 0.8028 (tpt170) REVERT: a 284 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8222 (mtp) REVERT: a 303 GLU cc_start: 0.6959 (tp30) cc_final: 0.6636 (tp30) REVERT: a 311 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7803 (t70) REVERT: a 326 LEU cc_start: 0.8137 (mt) cc_final: 0.7746 (mp) REVERT: a 348 GLN cc_start: 0.5075 (mt0) cc_final: 0.4140 (tt0) REVERT: a 410 MET cc_start: 0.8047 (mtp) cc_final: 0.7574 (ttm) REVERT: a 419 TYR cc_start: 0.5958 (OUTLIER) cc_final: 0.5193 (t80) REVERT: a 420 MET cc_start: 0.8009 (mmt) cc_final: 0.7367 (tpt) REVERT: H 5 GLN cc_start: 0.7178 (tp40) cc_final: 0.6808 (tp-100) REVERT: H 6 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6900 (mm-30) REVERT: H 53 ILE cc_start: 0.8458 (mt) cc_final: 0.8244 (mt) REVERT: H 90 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8256 (mtpp) REVERT: H 98 ASP cc_start: 0.7378 (m-30) cc_final: 0.6975 (m-30) REVERT: L 17 GLU cc_start: 0.7526 (mp0) cc_final: 0.7189 (mp0) REVERT: L 18 ARG cc_start: 0.8508 (ttm170) cc_final: 0.7543 (ttp80) REVERT: L 94 LEU cc_start: 0.7791 (tp) cc_final: 0.7160 (tt) REVERT: L 99 PHE cc_start: 0.7314 (m-80) cc_final: 0.6621 (m-80) REVERT: L 102 TYR cc_start: 0.8281 (m-80) cc_final: 0.8061 (m-80) REVERT: J 5 GLN cc_start: 0.7131 (tp40) cc_final: 0.6739 (tp-100) REVERT: J 30 PHE cc_start: 0.8337 (t80) cc_final: 0.8100 (t80) REVERT: J 43 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.8091 (mtm110) REVERT: J 52 TRP cc_start: 0.8024 (t60) cc_final: 0.7587 (t60) REVERT: J 98 ASP cc_start: 0.7058 (m-30) cc_final: 0.6666 (m-30) REVERT: K 5 THR cc_start: 0.7738 (m) cc_final: 0.7537 (p) REVERT: K 17 GLU cc_start: 0.8188 (mp0) cc_final: 0.7353 (mp0) REVERT: K 42 TYR cc_start: 0.8586 (m-80) cc_final: 0.7978 (m-80) REVERT: K 90 THR cc_start: 0.8785 (m) cc_final: 0.8551 (p) REVERT: K 94 LEU cc_start: 0.7574 (tp) cc_final: 0.7134 (tt) REVERT: K 99 PHE cc_start: 0.7644 (m-80) cc_final: 0.6977 (m-80) REVERT: h 5 GLN cc_start: 0.6971 (tp40) cc_final: 0.6501 (tp-100) REVERT: h 43 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8183 (mtm110) REVERT: h 53 ILE cc_start: 0.8477 (mt) cc_final: 0.7977 (mt) REVERT: h 85 ASN cc_start: 0.7381 (p0) cc_final: 0.7078 (p0) REVERT: h 87 PHE cc_start: 0.8438 (p90) cc_final: 0.8056 (p90) REVERT: l 17 GLU cc_start: 0.7939 (mp0) cc_final: 0.7586 (mp0) REVERT: l 90 THR cc_start: 0.8715 (m) cc_final: 0.8416 (p) REVERT: l 99 PHE cc_start: 0.7307 (m-80) cc_final: 0.6715 (m-80) outliers start: 55 outliers final: 36 residues processed: 304 average time/residue: 0.3313 time to fit residues: 145.1628 Evaluate side-chains 291 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 210 TRP 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 311 ASP 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 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 419 TYR Chi-restraints excluded: chain a residue 423 GLN 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 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 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 h residue 125 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 39 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 11 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 HIS ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.107013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082972 restraints weight = 37456.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086256 restraints weight = 20587.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088377 restraints weight = 14729.911| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5490 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= 0.171 Angle : 0.754 12.164 21390 Z= 0.353 Chirality : 0.043 0.251 2604 Planarity : 0.004 0.059 2514 Dihedral : 6.648 44.617 3903 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.69 % Rotamer: Outliers : 3.05 % Allowed : 15.14 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1731 helix: 1.15 (0.29), residues: 375 sheet: 0.14 (0.25), residues: 426 loop : -0.97 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 52 HIS 0.008 0.001 HIS c 305 PHE 0.023 0.002 PHE J 87 TYR 0.028 0.001 TYR c 419 ARG 0.013 0.001 ARG L 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 33) link_NAG-ASN : angle 1.64540 ( 99) link_ALPHA1-6 : bond 0.01025 ( 6) link_ALPHA1-6 : angle 1.58627 ( 18) link_BETA1-4 : bond 0.00748 ( 45) link_BETA1-4 : angle 2.36476 ( 135) link_ALPHA1-2 : bond 0.00120 ( 3) link_ALPHA1-2 : angle 2.05862 ( 9) link_ALPHA1-3 : bond 0.01520 ( 12) link_ALPHA1-3 : angle 3.33134 ( 36) hydrogen bonds : bond 0.03713 ( 552) hydrogen bonds : angle 5.02029 ( 1566) SS BOND : bond 0.00820 ( 27) SS BOND : angle 1.74371 ( 54) covalent geometry : bond 0.00384 (15516) covalent geometry : angle 0.70591 (21039) *********************** 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 308 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.8677 (ptt) cc_final: 0.8278 (pmm) REVERT: C 116 LYS cc_start: 0.9157 (mmtm) cc_final: 0.8845 (mmmt) REVERT: C 151 GLU cc_start: 0.8180 (pm20) cc_final: 0.7800 (pm20) REVERT: C 156 ASP cc_start: 0.7939 (t70) cc_final: 0.7002 (t0) REVERT: C 161 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8348 (ttpp) REVERT: C 194 MET cc_start: 0.8902 (tpp) cc_final: 0.8440 (ttp) REVERT: B 116 LYS cc_start: 0.9162 (mmtm) cc_final: 0.8920 (mmmt) REVERT: B 156 ASP cc_start: 0.8019 (t70) cc_final: 0.7363 (t0) REVERT: B 161 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8207 (ttpp) REVERT: c 282 ARG cc_start: 0.8577 (tpt90) cc_final: 0.7965 (tpm170) REVERT: c 311 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8034 (t0) REVERT: c 348 GLN cc_start: 0.4895 (mt0) cc_final: 0.4072 (tt0) REVERT: c 420 MET cc_start: 0.7585 (mmt) cc_final: 0.6705 (tpt) REVERT: A 116 LYS cc_start: 0.9173 (mmtm) cc_final: 0.8964 (mmmt) REVERT: A 125 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8684 (tppt) REVERT: A 151 GLU cc_start: 0.8095 (pm20) cc_final: 0.7858 (pt0) REVERT: A 161 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8386 (ttpp) REVERT: b 284 MET cc_start: 0.8348 (mtm) cc_final: 0.7745 (mtm) REVERT: b 332 MET cc_start: 0.7804 (tpp) cc_final: 0.7303 (tpp) REVERT: b 410 MET cc_start: 0.7956 (mmm) cc_final: 0.7632 (mmm) REVERT: b 420 MET cc_start: 0.7668 (mmt) cc_final: 0.7009 (tpt) REVERT: a 282 ARG cc_start: 0.8490 (tpt90) cc_final: 0.8057 (tpt170) REVERT: a 284 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8226 (mtp) REVERT: a 303 GLU cc_start: 0.7027 (tp30) cc_final: 0.6507 (tp30) REVERT: a 311 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7862 (t0) REVERT: a 326 LEU cc_start: 0.8218 (mt) cc_final: 0.7849 (mp) REVERT: a 332 MET cc_start: 0.7720 (tpp) cc_final: 0.7028 (tpp) REVERT: a 348 GLN cc_start: 0.5150 (mt0) cc_final: 0.4207 (tt0) REVERT: a 410 MET cc_start: 0.8076 (mtp) cc_final: 0.7576 (ttm) REVERT: a 419 TYR cc_start: 0.5967 (OUTLIER) cc_final: 0.5246 (t80) REVERT: a 420 MET cc_start: 0.7902 (mmt) cc_final: 0.7397 (tpt) REVERT: H 5 GLN cc_start: 0.7297 (tp40) cc_final: 0.6794 (tp-100) REVERT: H 51 GLU cc_start: 0.7382 (tt0) cc_final: 0.7175 (tt0) REVERT: H 90 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8293 (mtpp) REVERT: H 98 ASP cc_start: 0.7450 (m-30) cc_final: 0.7067 (m-30) REVERT: L 17 GLU cc_start: 0.7555 (mp0) cc_final: 0.7211 (mp0) REVERT: L 18 ARG cc_start: 0.8528 (ttm170) cc_final: 0.7556 (ttp80) REVERT: L 94 LEU cc_start: 0.7796 (tp) cc_final: 0.7151 (tt) REVERT: L 99 PHE cc_start: 0.7368 (m-80) cc_final: 0.6710 (m-80) REVERT: L 127 LYS cc_start: 0.7577 (pttt) cc_final: 0.7318 (ptpt) REVERT: J 5 GLN cc_start: 0.7067 (tp40) cc_final: 0.6706 (tp-100) REVERT: J 30 PHE cc_start: 0.8362 (t80) cc_final: 0.8070 (t80) REVERT: J 52 TRP cc_start: 0.7958 (t60) cc_final: 0.7429 (t60) REVERT: J 98 ASP cc_start: 0.7175 (m-30) cc_final: 0.6802 (m-30) REVERT: K 17 GLU cc_start: 0.8262 (mp0) cc_final: 0.7375 (mp0) REVERT: K 42 TYR cc_start: 0.8638 (m-80) cc_final: 0.8009 (m-80) REVERT: K 90 THR cc_start: 0.8835 (m) cc_final: 0.8557 (p) REVERT: K 94 LEU cc_start: 0.7504 (tp) cc_final: 0.7044 (tt) REVERT: K 99 PHE cc_start: 0.7676 (m-80) cc_final: 0.7065 (m-80) REVERT: K 102 TYR cc_start: 0.8249 (m-80) cc_final: 0.7923 (m-80) REVERT: h 5 GLN cc_start: 0.7016 (tp40) cc_final: 0.6667 (tp-100) REVERT: h 43 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8089 (mtm110) REVERT: h 52 TRP cc_start: 0.8010 (t60) cc_final: 0.7574 (t60) REVERT: h 53 ILE cc_start: 0.8502 (mt) cc_final: 0.7921 (mt) REVERT: h 85 ASN cc_start: 0.7353 (p0) cc_final: 0.7061 (p0) REVERT: h 87 PHE cc_start: 0.8555 (p90) cc_final: 0.8169 (p90) REVERT: l 17 GLU cc_start: 0.7920 (mp0) cc_final: 0.7554 (mp0) REVERT: l 90 THR cc_start: 0.8737 (m) cc_final: 0.8430 (p) REVERT: l 99 PHE cc_start: 0.7448 (m-80) cc_final: 0.6925 (m-80) outliers start: 47 outliers final: 33 residues processed: 282 average time/residue: 0.2988 time to fit residues: 124.0520 Evaluate side-chains 290 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 84 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 411 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 287 GLU 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 419 TYR Chi-restraints excluded: chain a residue 423 GLN Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 90 LYS 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 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 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 5 THR 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 93 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 150 optimal weight: 0.0980 chunk 144 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.105081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082070 restraints weight = 37355.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085498 restraints weight = 19195.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087800 restraints weight = 13127.055| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5619 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 : 0.705 10.241 21390 Z= 0.331 Chirality : 0.043 0.253 2604 Planarity : 0.004 0.052 2514 Dihedral : 6.309 36.812 3903 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.92 % Allowed : 15.92 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1731 helix: 1.27 (0.29), residues: 375 sheet: 0.16 (0.25), residues: 423 loop : -0.92 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 52 HIS 0.008 0.001 HIS c 305 PHE 0.024 0.001 PHE J 87 TYR 0.035 0.001 TYR c 419 ARG 0.012 0.000 ARG L 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 33) link_NAG-ASN : angle 1.52657 ( 99) link_ALPHA1-6 : bond 0.01115 ( 6) link_ALPHA1-6 : angle 1.53228 ( 18) link_BETA1-4 : bond 0.00779 ( 45) link_BETA1-4 : angle 2.26632 ( 135) link_ALPHA1-2 : bond 0.00087 ( 3) link_ALPHA1-2 : angle 2.11570 ( 9) link_ALPHA1-3 : bond 0.01467 ( 12) link_ALPHA1-3 : angle 3.29320 ( 36) hydrogen bonds : bond 0.03441 ( 552) hydrogen bonds : angle 4.92274 ( 1566) SS BOND : bond 0.00714 ( 27) SS BOND : angle 1.48418 ( 54) covalent geometry : bond 0.00284 (15516) covalent geometry : angle 0.65768 (21039) *********************** 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 317 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 272 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 MET cc_start: 0.8321 (mmm) cc_final: 0.8021 (mmm) REVERT: C 82 MET cc_start: 0.8605 (ptt) cc_final: 0.8229 (pmm) REVERT: C 151 GLU cc_start: 0.8207 (pm20) cc_final: 0.7793 (pm20) REVERT: C 156 ASP cc_start: 0.7882 (t70) cc_final: 0.6875 (t0) REVERT: C 161 LYS cc_start: 0.8710 (ttmt) cc_final: 0.8299 (ttpp) REVERT: C 194 MET cc_start: 0.8930 (tpp) cc_final: 0.8507 (ttp) REVERT: B 67 GLU cc_start: 0.7208 (tt0) cc_final: 0.6889 (tm-30) REVERT: B 116 LYS cc_start: 0.9073 (mmtm) cc_final: 0.8857 (mmmt) REVERT: B 156 ASP cc_start: 0.7997 (t70) cc_final: 0.7309 (t0) REVERT: B 161 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8161 (ttpp) REVERT: c 282 ARG cc_start: 0.8646 (tpt90) cc_final: 0.8095 (tpm170) REVERT: c 311 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7928 (t0) REVERT: c 348 GLN cc_start: 0.4632 (mt0) cc_final: 0.3910 (tt0) REVERT: c 420 MET cc_start: 0.7442 (mmt) cc_final: 0.6590 (tpt) REVERT: A 116 LYS cc_start: 0.9123 (mmtm) cc_final: 0.8920 (mmmt) REVERT: A 125 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8659 (tppt) REVERT: A 194 MET cc_start: 0.8739 (tpp) cc_final: 0.8190 (ttm) REVERT: b 284 MET cc_start: 0.8361 (mtm) cc_final: 0.7668 (mtm) REVERT: b 332 MET cc_start: 0.7757 (tpp) cc_final: 0.7236 (tpp) REVERT: b 419 TYR cc_start: 0.6987 (t80) cc_final: 0.6071 (t80) REVERT: b 420 MET cc_start: 0.7636 (mmt) cc_final: 0.7006 (tpt) REVERT: a 282 ARG cc_start: 0.8470 (tpt90) cc_final: 0.8048 (tpt170) REVERT: a 284 MET cc_start: 0.8459 (mtp) cc_final: 0.8185 (mtp) REVERT: a 303 GLU cc_start: 0.7065 (tp30) cc_final: 0.6714 (tp30) REVERT: a 311 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7836 (t0) REVERT: a 326 LEU cc_start: 0.8189 (mt) cc_final: 0.7779 (mp) REVERT: a 332 MET cc_start: 0.7660 (tpp) cc_final: 0.6890 (tpp) REVERT: a 348 GLN cc_start: 0.4853 (mt0) cc_final: 0.3968 (tt0) REVERT: a 410 MET cc_start: 0.7984 (mtp) cc_final: 0.7477 (ttm) REVERT: a 419 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.5248 (t80) REVERT: a 420 MET cc_start: 0.7957 (mmt) cc_final: 0.7446 (tpt) REVERT: H 5 GLN cc_start: 0.7221 (tp40) cc_final: 0.6675 (tp-100) REVERT: H 90 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8292 (mtpp) REVERT: H 95 THR cc_start: 0.7985 (t) cc_final: 0.7689 (p) REVERT: H 98 ASP cc_start: 0.7383 (m-30) cc_final: 0.6923 (m-30) REVERT: L 17 GLU cc_start: 0.7590 (mp0) cc_final: 0.7220 (mp0) REVERT: L 18 ARG cc_start: 0.8480 (ttm170) cc_final: 0.7531 (ttp80) REVERT: L 94 LEU cc_start: 0.7756 (tp) cc_final: 0.7123 (tt) REVERT: L 99 PHE cc_start: 0.7539 (m-80) cc_final: 0.6867 (m-80) REVERT: L 127 LYS cc_start: 0.7620 (pttt) cc_final: 0.7328 (ptpt) REVERT: J 5 GLN cc_start: 0.6950 (tp40) cc_final: 0.6591 (tp-100) REVERT: J 30 PHE cc_start: 0.8262 (t80) cc_final: 0.7993 (t80) REVERT: J 43 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7864 (mtm-85) REVERT: J 52 TRP cc_start: 0.7841 (t60) cc_final: 0.7421 (t60) REVERT: J 75 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7848 (mtm180) REVERT: J 98 ASP cc_start: 0.7031 (m-30) cc_final: 0.6653 (m-30) REVERT: J 99 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8226 (p) REVERT: K 17 GLU cc_start: 0.8202 (mp0) cc_final: 0.7332 (mp0) REVERT: K 42 TYR cc_start: 0.8410 (m-80) cc_final: 0.7880 (m-80) REVERT: K 90 THR cc_start: 0.8741 (m) cc_final: 0.8499 (p) REVERT: K 94 LEU cc_start: 0.7403 (tp) cc_final: 0.6918 (tt) REVERT: K 99 PHE cc_start: 0.7492 (m-80) cc_final: 0.6824 (m-80) REVERT: K 102 TYR cc_start: 0.7955 (m-80) cc_final: 0.7735 (m-80) REVERT: h 5 GLN cc_start: 0.7078 (tp40) cc_final: 0.6650 (tp-100) REVERT: h 43 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7627 (mtm110) REVERT: h 52 TRP cc_start: 0.7892 (t60) cc_final: 0.7440 (t60) REVERT: h 53 ILE cc_start: 0.8253 (mt) cc_final: 0.7620 (mt) REVERT: h 87 PHE cc_start: 0.8444 (p90) cc_final: 0.8061 (p90) REVERT: l 17 GLU cc_start: 0.7878 (mp0) cc_final: 0.7513 (mp0) REVERT: l 90 THR cc_start: 0.8746 (m) cc_final: 0.8384 (p) REVERT: l 99 PHE cc_start: 0.7279 (m-80) cc_final: 0.6709 (m-80) outliers start: 45 outliers final: 31 residues processed: 291 average time/residue: 0.2935 time to fit residues: 124.0935 Evaluate side-chains 295 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 84 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 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 345 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 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 419 TYR Chi-restraints excluded: chain a residue 423 GLN Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 90 LYS 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 5 THR 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 18 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 150 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 135 optimal weight: 0.0770 chunk 98 optimal weight: 0.8980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 305 HIS ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.105866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082913 restraints weight = 37617.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086407 restraints weight = 19324.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.088690 restraints weight = 13161.455| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15642 Z= 0.125 Angle : 0.710 11.692 21390 Z= 0.333 Chirality : 0.042 0.244 2604 Planarity : 0.004 0.051 2514 Dihedral : 6.049 36.104 3903 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.53 % Allowed : 16.57 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1731 helix: 1.35 (0.29), residues: 375 sheet: 0.19 (0.25), residues: 423 loop : -0.93 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 52 HIS 0.007 0.001 HIS c 305 PHE 0.025 0.001 PHE J 87 TYR 0.020 0.001 TYR a 419 ARG 0.011 0.000 ARG L 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 33) link_NAG-ASN : angle 1.44960 ( 99) link_ALPHA1-6 : bond 0.01168 ( 6) link_ALPHA1-6 : angle 1.48050 ( 18) link_BETA1-4 : bond 0.00769 ( 45) link_BETA1-4 : angle 2.21268 ( 135) link_ALPHA1-2 : bond 0.00056 ( 3) link_ALPHA1-2 : angle 2.06548 ( 9) link_ALPHA1-3 : bond 0.01429 ( 12) link_ALPHA1-3 : angle 3.17281 ( 36) hydrogen bonds : bond 0.03302 ( 552) hydrogen bonds : angle 4.84987 ( 1566) SS BOND : bond 0.00562 ( 27) SS BOND : angle 1.42522 ( 54) covalent geometry : bond 0.00272 (15516) covalent geometry : angle 0.66751 (21039) ********************** 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 314 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.8539 (ptt) cc_final: 0.8163 (pmm) REVERT: C 151 GLU cc_start: 0.8206 (pm20) cc_final: 0.7803 (pm20) REVERT: C 156 ASP cc_start: 0.7852 (t70) cc_final: 0.6864 (t0) REVERT: C 161 LYS cc_start: 0.8704 (ttmt) cc_final: 0.8298 (ttpp) REVERT: C 194 MET cc_start: 0.8942 (tpp) cc_final: 0.8501 (ttp) REVERT: B 116 LYS cc_start: 0.9076 (mmtm) cc_final: 0.8861 (mmmt) REVERT: B 156 ASP cc_start: 0.7926 (t70) cc_final: 0.7234 (t0) REVERT: B 161 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8139 (ttpp) REVERT: c 282 ARG cc_start: 0.8592 (tpt90) cc_final: 0.8041 (tpm170) REVERT: c 303 GLU cc_start: 0.6725 (tp30) cc_final: 0.5939 (tp30) REVERT: c 348 GLN cc_start: 0.4625 (mt0) cc_final: 0.3984 (tt0) REVERT: c 419 TYR cc_start: 0.7089 (t80) cc_final: 0.6816 (t80) REVERT: c 420 MET cc_start: 0.7473 (mmt) cc_final: 0.6644 (tpt) REVERT: A 125 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8647 (tppt) REVERT: A 151 GLU cc_start: 0.8238 (pm20) cc_final: 0.7960 (pt0) REVERT: A 194 MET cc_start: 0.8690 (tpp) cc_final: 0.8114 (ttm) REVERT: b 284 MET cc_start: 0.8322 (mtm) cc_final: 0.7635 (mtm) REVERT: b 332 MET cc_start: 0.7729 (tpp) cc_final: 0.7237 (tpp) REVERT: b 419 TYR cc_start: 0.7026 (t80) cc_final: 0.6096 (t80) REVERT: b 420 MET cc_start: 0.7710 (mmt) cc_final: 0.7143 (tpt) REVERT: a 282 ARG cc_start: 0.8467 (tpt90) cc_final: 0.8034 (tpt170) REVERT: a 284 MET cc_start: 0.8414 (mtp) cc_final: 0.8147 (mtp) REVERT: a 303 GLU cc_start: 0.7016 (tp30) cc_final: 0.6523 (tp30) REVERT: a 311 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7870 (t0) REVERT: a 326 LEU cc_start: 0.8308 (mt) cc_final: 0.8081 (mp) REVERT: a 332 MET cc_start: 0.7718 (tpp) cc_final: 0.6928 (tpp) REVERT: a 348 GLN cc_start: 0.4578 (mt0) cc_final: 0.3911 (tt0) REVERT: a 410 MET cc_start: 0.7975 (mtp) cc_final: 0.7470 (ttm) REVERT: a 419 TYR cc_start: 0.5839 (OUTLIER) cc_final: 0.5073 (t80) REVERT: a 420 MET cc_start: 0.7958 (mmt) cc_final: 0.7453 (tpt) REVERT: H 5 GLN cc_start: 0.7251 (tp40) cc_final: 0.6871 (tp-100) REVERT: H 95 THR cc_start: 0.7985 (t) cc_final: 0.7681 (p) REVERT: H 98 ASP cc_start: 0.7298 (m-30) cc_final: 0.6885 (m-30) REVERT: L 17 GLU cc_start: 0.7615 (mp0) cc_final: 0.6817 (mp0) REVERT: L 18 ARG cc_start: 0.8475 (ttm170) cc_final: 0.7530 (ttp80) REVERT: L 94 LEU cc_start: 0.7704 (tp) cc_final: 0.6930 (tt) REVERT: L 99 PHE cc_start: 0.7432 (m-80) cc_final: 0.6632 (m-80) REVERT: J 5 GLN cc_start: 0.6987 (tp40) cc_final: 0.6645 (tp-100) REVERT: J 30 PHE cc_start: 0.8260 (t80) cc_final: 0.7995 (t80) REVERT: J 52 TRP cc_start: 0.7913 (t60) cc_final: 0.7490 (t60) REVERT: J 75 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7909 (mtm180) REVERT: J 98 ASP cc_start: 0.7052 (m-30) cc_final: 0.6682 (m-30) REVERT: J 99 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8163 (p) REVERT: K 17 GLU cc_start: 0.8210 (mp0) cc_final: 0.7368 (mp0) REVERT: K 42 TYR cc_start: 0.8286 (m-80) cc_final: 0.7816 (m-80) REVERT: K 90 THR cc_start: 0.8714 (m) cc_final: 0.8485 (p) REVERT: K 94 LEU cc_start: 0.7386 (tp) cc_final: 0.6886 (tt) REVERT: K 99 PHE cc_start: 0.7426 (m-80) cc_final: 0.6853 (m-80) REVERT: h 5 GLN cc_start: 0.7100 (tp40) cc_final: 0.6687 (tp-100) REVERT: h 43 ARG cc_start: 0.7915 (ttp80) cc_final: 0.7497 (mtm110) REVERT: h 52 TRP cc_start: 0.7892 (t60) cc_final: 0.7429 (t60) REVERT: h 53 ILE cc_start: 0.8246 (mt) cc_final: 0.7615 (mt) REVERT: h 85 ASN cc_start: 0.7824 (p0) cc_final: 0.7147 (p0) REVERT: h 87 PHE cc_start: 0.8393 (p90) cc_final: 0.8084 (p90) REVERT: h 118 TRP cc_start: 0.8383 (m100) cc_final: 0.7989 (m100) REVERT: l 17 GLU cc_start: 0.7891 (mp0) cc_final: 0.7520 (mp0) REVERT: l 90 THR cc_start: 0.8673 (m) cc_final: 0.8297 (p) outliers start: 39 outliers final: 32 residues processed: 292 average time/residue: 0.2934 time to fit residues: 124.9156 Evaluate side-chains 297 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 210 TRP 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 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 b residue 323 ILE Chi-restraints excluded: chain b residue 345 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 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 419 TYR Chi-restraints excluded: chain a residue 423 GLN 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 5 THR 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 8 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.104893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.081951 restraints weight = 37677.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085391 restraints weight = 19201.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087661 restraints weight = 13097.884| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15642 Z= 0.145 Angle : 0.721 9.819 21390 Z= 0.338 Chirality : 0.042 0.240 2604 Planarity : 0.004 0.056 2514 Dihedral : 6.047 34.891 3903 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.47 % Allowed : 16.70 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1731 helix: 1.37 (0.29), residues: 375 sheet: 0.17 (0.26), residues: 420 loop : -0.95 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 52 HIS 0.009 0.001 HIS L 44 PHE 0.025 0.002 PHE J 87 TYR 0.020 0.001 TYR a 419 ARG 0.015 0.000 ARG L 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 33) link_NAG-ASN : angle 1.47910 ( 99) link_ALPHA1-6 : bond 0.01141 ( 6) link_ALPHA1-6 : angle 1.53961 ( 18) link_BETA1-4 : bond 0.00735 ( 45) link_BETA1-4 : angle 2.21629 ( 135) link_ALPHA1-2 : bond 0.00080 ( 3) link_ALPHA1-2 : angle 2.02627 ( 9) link_ALPHA1-3 : bond 0.01392 ( 12) link_ALPHA1-3 : angle 3.18633 ( 36) hydrogen bonds : bond 0.03435 ( 552) hydrogen bonds : angle 4.86351 ( 1566) SS BOND : bond 0.00618 ( 27) SS BOND : angle 1.47336 ( 54) covalent geometry : bond 0.00326 (15516) covalent geometry : angle 0.67793 (21039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5427.01 seconds wall clock time: 99 minutes 54.71 seconds (5994.71 seconds total)