Starting phenix.real_space_refine on Sat May 17 05:47:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejh_28182/05_2025/8ejh_28182.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejh_28182/05_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_28182/05_2025/8ejh_28182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejh_28182/05_2025/8ejh_28182.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejh_28182/05_2025/8ejh_28182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejh_28182/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.07, per 1000 atoms: 0.66 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: 5.58 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: 2.04 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: 5.61 Time building geometry restraints manager: 6.20 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.900 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.050 ------------------------------------------------------------------------------- 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 : 1.677 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: 0.3285 time to fit residues: 247.1445 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 : 1.879 ------------------------------------------------------------------------------- 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 = 0.084924 restraints weight = 36891.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088527 restraints weight = 19891.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090897 restraints weight = 13789.176| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 : 1.596 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: 0.7776 (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: 0.9111 (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: 0.8414 (ttmt) cc_final: 0.7639 (tptt) REVERT: c 282 ARG cc_start: 0.8429 (tpt90) cc_final: 0.7880 (tpm170) REVERT: c 284 MET cc_start: 0.8309 (mtm) cc_final: 0.8074 (mtm) REVERT: c 303 GLU cc_start: 0.6087 (tp30) cc_final: 0.5532 (tp30) REVERT: c 351 MET cc_start: 0.8826 (tpp) cc_final: 0.8574 (tpp) REVERT: c 419 TYR cc_start: 0.7583 (t80) cc_final: 0.7336 (t80) REVERT: c 420 MET cc_start: 0.7352 (mmt) cc_final: 0.6275 (tpt) REVERT: A 96 MET cc_start: 0.7800 (mmm) cc_final: 0.7391 (mmm) REVERT: A 116 LYS cc_start: 0.8697 (mmtm) cc_final: 0.8372 (mmmt) REVERT: A 134 MET cc_start: 0.9423 (tpp) cc_final: 0.9080 (tpp) REVERT: A 156 ASP cc_start: 0.8056 (p0) cc_final: 0.7761 (p0) REVERT: b 284 MET cc_start: 0.8236 (mtm) cc_final: 0.7614 (mtm) REVERT: b 303 GLU cc_start: 0.6223 (tp30) cc_final: 0.5769 (tp30) REVERT: b 305 HIS cc_start: 0.7325 (m90) cc_final: 0.6884 (m-70) REVERT: b 332 MET cc_start: 0.7522 (mmp) cc_final: 0.7282 (mmm) REVERT: b 420 MET cc_start: 0.7360 (mmt) cc_final: 0.6920 (tpt) REVERT: b 423 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7786 (mp10) REVERT: a 282 ARG cc_start: 0.8219 (tpt90) cc_final: 0.7934 (tpm170) REVERT: a 284 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8011 (mtp) REVERT: a 306 ASP cc_start: 0.8425 (p0) cc_final: 0.8174 (p0) REVERT: a 326 LEU cc_start: 0.7885 (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: 0.8819 (m-40) cc_final: 0.8411 (m110) REVERT: a 420 MET cc_start: 0.7457 (mmt) cc_final: 0.6894 (tpt) REVERT: H 6 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6401 (mm-30) REVERT: H 13 LEU cc_start: 0.7255 (mt) cc_final: 0.7036 (pp) REVERT: H 43 ARG cc_start: 0.8382 (ttp-170) cc_final: 0.8164 (ttp80) REVERT: H 51 GLU cc_start: 0.7253 (mt-10) cc_final: 0.7002 (tt0) REVERT: H 78 ILE cc_start: 0.8418 (mt) cc_final: 0.8132 (tp) REVERT: H 98 ASP cc_start: 0.7224 (m-30) cc_final: 0.6810 (m-30) REVERT: H 112 TYR cc_start: 0.7881 (p90) cc_final: 0.7152 (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: 0.8211 (m) cc_final: 0.7790 (p) REVERT: L 94 LEU cc_start: 0.7675 (tp) cc_final: 0.6943 (tt) REVERT: L 99 PHE cc_start: 0.6691 (m-80) cc_final: 0.5659 (m-80) REVERT: L 125 GLU cc_start: 0.6703 (tt0) cc_final: 0.6348 (tt0) REVERT: J 43 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7813 (ttp-170) REVERT: J 52 TRP cc_start: 0.7689 (t60) cc_final: 0.7416 (t60) REVERT: J 98 ASP cc_start: 0.6923 (m-30) cc_final: 0.6523 (m-30) REVERT: J 122 THR cc_start: 0.7012 (m) cc_final: 0.6765 (p) REVERT: K 5 THR cc_start: 0.7923 (m) cc_final: 0.7704 (p) REVERT: K 18 ARG cc_start: 0.8379 (ttm170) cc_final: 0.7724 (ttp80) REVERT: K 90 THR cc_start: 0.8070 (m) cc_final: 0.7788 (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: 0.6368 (m-80) REVERT: h 43 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7835 (ttp80) REVERT: h 53 ILE cc_start: 0.8125 (mt) cc_final: 0.7826 (mt) REVERT: h 78 ILE cc_start: 0.8343 (mt) cc_final: 0.7767 (tp) REVERT: h 87 PHE cc_start: 0.8479 (p90) cc_final: 0.7875 (p90) REVERT: h 112 TYR cc_start: 0.8157 (p90) cc_final: 0.7802 (p90) REVERT: l 17 GLU cc_start: 0.7408 (mp0) cc_final: 0.6990 (mp0) REVERT: l 18 ARG cc_start: 0.8616 (ttm170) cc_final: 0.7811 (ttp80) REVERT: l 90 THR cc_start: 0.8134 (m) cc_final: 0.7743 (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: 0.2996 time to fit residues: 162.0661 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 : 1.811 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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** ** 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 = 0.3698 r_free = 0.3698 target = 0.105514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082298 restraints weight = 36432.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.085677 restraints weight = 18789.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087972 restraints weight = 12875.199| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15642 Z= 0.196 Angle : 0.831 11.911 21390 Z= 0.389 Chirality : 0.047 0.243 2604 Planarity : 0.004 0.038 2514 Dihedral : 10.264 61.288 3903 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.31 % Allowed : 12.09 % Favored : 84.60 % 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 (0.20), residues: 1731 helix: 0.72 (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 0.039 0.002 TRP H 52 HIS 0.007 0.001 HIS B 230 PHE 0.033 0.002 PHE J 87 TYR 0.027 0.002 TYR a 419 ARG 0.004 0.001 ARG a 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 33) link_NAG-ASN : angle 2.04123 ( 99) link_ALPHA1-6 : bond 0.00572 ( 6) link_ALPHA1-6 : angle 1.75491 ( 18) link_BETA1-4 : bond 0.00908 ( 45) link_BETA1-4 : angle 3.08611 ( 135) link_ALPHA1-2 : bond 0.00159 ( 3) link_ALPHA1-2 : angle 1.91003 ( 9) link_ALPHA1-3 : bond 0.02002 ( 12) link_ALPHA1-3 : angle 3.51151 ( 36) hydrogen bonds : bond 0.04578 ( 552) hydrogen bonds : angle 5.39593 ( 1566) SS BOND : bond 0.00941 ( 27) SS BOND : angle 1.75092 ( 54) covalent geometry : bond 0.00425 (15516) covalent geometry : angle 0.76653 (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 366 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 1.719 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: 0.7401 (pm20) cc_final: 0.7128 (pm20) REVERT: C 96 MET cc_start: 0.7871 (mmm) cc_final: 0.7663 (mmm) REVERT: C 156 ASP cc_start: 0.7727 (t70) cc_final: 0.6637 (t0) REVERT: C 161 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8249 (ttpp) REVERT: C 228 GLU cc_start: 0.8207 (mp0) cc_final: 0.8006 (mp0) REVERT: B 116 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8777 (mmmt) REVERT: B 156 ASP cc_start: 0.7893 (t70) cc_final: 0.7647 (t0) REVERT: B 161 LYS cc_start: 0.8568 (ttmt) cc_final: 0.7882 (tptt) REVERT: c 282 ARG cc_start: 0.8549 (tpt90) cc_final: 0.7906 (tpm170) REVERT: c 303 GLU cc_start: 0.6325 (tp30) cc_final: 0.5241 (tp30) REVERT: c 326 LEU cc_start: 0.7947 (mp) cc_final: 0.7516 (tp) REVERT: c 351 MET cc_start: 0.8910 (tpp) cc_final: 0.8627 (tpp) REVERT: c 420 MET cc_start: 0.7407 (mmt) cc_final: 0.6412 (tpt) REVERT: A 96 MET cc_start: 0.7950 (mmm) cc_final: 0.7731 (mmm) REVERT: A 116 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8771 (mmmt) REVERT: A 156 ASP cc_start: 0.8006 (p0) cc_final: 0.7710 (p0) REVERT: A 161 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8042 (tptt) REVERT: A 194 MET cc_start: 0.8909 (tpp) cc_final: 0.8685 (tpp) REVERT: A 245 LEU cc_start: 0.8550 (tp) cc_final: 0.8222 (tp) REVERT: b 284 MET cc_start: 0.8205 (mtm) cc_final: 0.7739 (mtm) REVERT: b 303 GLU cc_start: 0.6602 (tp30) cc_final: 0.6332 (tp30) REVERT: b 418 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8486 (mt-10) REVERT: b 419 TYR cc_start: 0.6876 (t80) cc_final: 0.6102 (t80) REVERT: b 420 MET cc_start: 0.7735 (mmt) cc_final: 0.6979 (tpt) REVERT: a 284 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8092 (mtp) REVERT: a 303 GLU cc_start: 0.6429 (tp30) cc_final: 0.6091 (tp30) REVERT: a 306 ASP cc_start: 0.8306 (p0) cc_final: 0.8082 (p0) REVERT: a 348 GLN cc_start: 0.5120 (mt0) cc_final: 0.4314 (tt0) REVERT: a 420 MET cc_start: 0.8066 (mmt) cc_final: 0.7541 (tpt) REVERT: H 13 LEU cc_start: 0.7430 (mt) cc_final: 0.7180 (pp) REVERT: H 53 ILE cc_start: 0.8271 (mt) cc_final: 0.7899 (mt) REVERT: H 98 ASP cc_start: 0.7419 (m-30) cc_final: 0.6989 (m-30) REVERT: H 110 TYR cc_start: 0.8415 (t80) cc_final: 0.7945 (t80) REVERT: H 112 TYR cc_start: 0.8188 (p90) cc_final: 0.7259 (p90) REVERT: L 17 GLU cc_start: 0.7187 (mp0) cc_final: 0.6890 (mp0) REVERT: L 18 ARG cc_start: 0.8378 (ttm170) cc_final: 0.7638 (ttp80) REVERT: L 90 THR cc_start: 0.8388 (m) cc_final: 0.8062 (p) REVERT: L 94 LEU cc_start: 0.7842 (tp) cc_final: 0.7157 (tt) REVERT: L 99 PHE cc_start: 0.7171 (m-80) cc_final: 0.6284 (m-80) REVERT: L 122 THR cc_start: 0.7967 (p) cc_final: 0.7723 (p) REVERT: J 5 GLN cc_start: 0.7213 (tp40) cc_final: 0.6752 (tp-100) REVERT: J 19 LEU cc_start: 0.8549 (tp) cc_final: 0.8331 (tt) REVERT: J 52 TRP cc_start: 0.7955 (t60) cc_final: 0.7302 (t60) REVERT: J 98 ASP cc_start: 0.7146 (m-30) cc_final: 0.6670 (m-30) REVERT: K 5 THR cc_start: 0.7864 (m) cc_final: 0.7652 (p) REVERT: K 17 GLU cc_start: 0.7651 (mp0) cc_final: 0.7317 (mp0) REVERT: K 90 THR cc_start: 0.8376 (m) cc_final: 0.8084 (p) REVERT: K 94 LEU cc_start: 0.7733 (tp) cc_final: 0.7396 (tt) REVERT: K 99 PHE cc_start: 0.7332 (m-80) cc_final: 0.6768 (m-80) REVERT: h 43 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8064 (mtm110) REVERT: h 52 TRP cc_start: 0.7992 (t60) cc_final: 0.7660 (t60) REVERT: h 53 ILE cc_start: 0.8293 (mt) cc_final: 0.7781 (mt) REVERT: h 87 PHE cc_start: 0.8375 (p90) cc_final: 0.8174 (p90) REVERT: h 98 ASP cc_start: 0.7108 (m-30) cc_final: 0.6899 (m-30) REVERT: l 17 GLU cc_start: 0.7690 (mp0) cc_final: 0.7362 (mp0) REVERT: l 18 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7662 (ttp80) REVERT: l 90 THR cc_start: 0.8348 (m) cc_final: 0.7950 (p) REVERT: l 94 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7457 (tt) REVERT: l 99 PHE cc_start: 0.7270 (m-80) cc_final: 0.6472 (m-80) outliers start: 51 outliers final: 29 residues processed: 336 average time/residue: 0.2926 time to fit residues: 141.9035 Evaluate side-chains 313 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP 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 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: 3.9990 chunk 127 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 113 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 = 0.3669 r_free = 0.3669 target = 0.104451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081098 restraints weight = 36676.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084442 restraints weight = 19233.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086681 restraints weight = 13275.509| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15642 Z= 0.192 Angle : 0.784 11.359 21390 Z= 0.368 Chirality : 0.045 0.262 2604 Planarity : 0.004 0.035 2514 Dihedral : 8.161 53.033 3903 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.12 % Allowed : 13.32 % Favored : 83.56 % 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: -0.19 (0.20), residues: 1731 helix: 1.03 (0.28), residues: 375 sheet: 0.24 (0.25), residues: 411 loop : -0.75 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP H 52 HIS 0.005 0.001 HIS B 230 PHE 0.012 0.002 PHE H 87 TYR 0.021 0.002 TYR a 419 ARG 0.002 0.001 ARG a 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 33) link_NAG-ASN : angle 1.90878 ( 99) link_ALPHA1-6 : bond 0.00761 ( 6) link_ALPHA1-6 : angle 1.75879 ( 18) link_BETA1-4 : bond 0.00801 ( 45) link_BETA1-4 : angle 2.76903 ( 135) link_ALPHA1-2 : bond 0.00107 ( 3) link_ALPHA1-2 : angle 1.95338 ( 9) link_ALPHA1-3 : bond 0.01930 ( 12) link_ALPHA1-3 : angle 3.27216 ( 36) hydrogen bonds : bond 0.04146 ( 552) hydrogen bonds : angle 5.24979 ( 1566) SS BOND : bond 0.00745 ( 27) SS BOND : angle 2.36136 ( 54) covalent geometry : bond 0.00432 (15516) covalent geometry : angle 0.72213 (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 348 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 300 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7523 (pm20) cc_final: 0.7323 (pm20) REVERT: C 116 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8819 (mmmt) REVERT: C 156 ASP cc_start: 0.7930 (t70) cc_final: 0.6858 (t0) REVERT: C 161 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8286 (ttpp) REVERT: C 194 MET cc_start: 0.9114 (tpp) cc_final: 0.8250 (ttp) REVERT: B 116 LYS cc_start: 0.9134 (mmtm) cc_final: 0.8846 (mmmt) REVERT: B 156 ASP cc_start: 0.8022 (t70) cc_final: 0.7531 (t0) REVERT: B 161 LYS cc_start: 0.8605 (ttmt) cc_final: 0.7960 (tptt) REVERT: c 282 ARG cc_start: 0.8517 (tpt90) cc_final: 0.7923 (tpm170) REVERT: c 284 MET cc_start: 0.8368 (mtm) cc_final: 0.8143 (mtm) REVERT: c 326 LEU cc_start: 0.8166 (mp) cc_final: 0.7965 (mp) REVERT: c 351 MET cc_start: 0.8910 (tpp) cc_final: 0.8636 (tpp) REVERT: c 420 MET cc_start: 0.7389 (mmt) cc_final: 0.6460 (tpt) REVERT: A 80 MET cc_start: 0.8840 (mmt) cc_final: 0.8093 (mmm) REVERT: A 96 MET cc_start: 0.7872 (mmm) cc_final: 0.7663 (mmm) REVERT: A 116 LYS cc_start: 0.9099 (mmtm) cc_final: 0.8828 (mmmt) REVERT: A 156 ASP cc_start: 0.7970 (p0) cc_final: 0.7698 (p0) REVERT: A 161 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8444 (ttpp) REVERT: b 284 MET cc_start: 0.8232 (mtm) cc_final: 0.7685 (mtm) REVERT: b 311 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8182 (t0) REVERT: b 332 MET cc_start: 0.7778 (tpp) cc_final: 0.7508 (tpp) REVERT: b 420 MET cc_start: 0.7708 (mmt) cc_final: 0.7292 (tpt) REVERT: a 282 ARG cc_start: 0.8526 (tpt90) cc_final: 0.8033 (tpm170) REVERT: a 284 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8008 (mtp) REVERT: a 311 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7503 (t0) REVERT: a 326 LEU cc_start: 0.8282 (mt) cc_final: 0.7530 (mt) REVERT: a 332 MET cc_start: 0.7714 (tpp) cc_final: 0.7460 (tpp) REVERT: a 348 GLN cc_start: 0.5118 (mt0) cc_final: 0.4314 (tt0) REVERT: a 420 MET cc_start: 0.7888 (mmt) cc_final: 0.7340 (tpt) REVERT: H 43 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8355 (mtm110) REVERT: H 53 ILE cc_start: 0.8370 (mt) cc_final: 0.7863 (mt) REVERT: H 90 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8177 (mtpp) REVERT: H 98 ASP cc_start: 0.7464 (m-30) cc_final: 0.7085 (m-30) REVERT: L 17 GLU cc_start: 0.7311 (mp0) cc_final: 0.7014 (mp0) REVERT: L 18 ARG cc_start: 0.8400 (ttm170) cc_final: 0.7548 (ttp80) REVERT: L 90 THR cc_start: 0.8502 (m) cc_final: 0.8235 (p) REVERT: L 94 LEU cc_start: 0.7783 (tp) cc_final: 0.7097 (tt) REVERT: L 99 PHE cc_start: 0.7340 (m-80) cc_final: 0.6534 (m-80) REVERT: J 5 GLN cc_start: 0.7184 (tp40) cc_final: 0.6720 (tp-100) REVERT: J 43 ARG cc_start: 0.8488 (ttp-170) cc_final: 0.8048 (mtm110) REVERT: J 52 TRP cc_start: 0.7983 (t60) cc_final: 0.7306 (t60) REVERT: J 98 ASP cc_start: 0.7158 (m-30) cc_final: 0.6675 (m-30) REVERT: K 5 THR cc_start: 0.7847 (m) cc_final: 0.7578 (p) REVERT: K 17 GLU cc_start: 0.7796 (mp0) cc_final: 0.6883 (mp0) REVERT: K 90 THR cc_start: 0.8658 (m) cc_final: 0.8387 (p) REVERT: K 94 LEU cc_start: 0.7699 (tp) cc_final: 0.7292 (tt) REVERT: K 99 PHE cc_start: 0.7421 (m-80) cc_final: 0.6871 (m-80) REVERT: h 13 LEU cc_start: 0.7136 (mt) cc_final: 0.6912 (pp) REVERT: h 43 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7986 (mtm110) REVERT: h 52 TRP cc_start: 0.8074 (t60) cc_final: 0.7681 (t60) REVERT: h 53 ILE cc_start: 0.8324 (mt) cc_final: 0.7714 (mt) REVERT: h 87 PHE cc_start: 0.8447 (p90) cc_final: 0.7956 (p90) REVERT: h 98 ASP cc_start: 0.7085 (m-30) cc_final: 0.6749 (m-30) REVERT: l 17 GLU cc_start: 0.7786 (mp0) cc_final: 0.7454 (mp0) REVERT: l 90 THR cc_start: 0.8560 (m) cc_final: 0.8190 (p) REVERT: l 94 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7475 (tt) REVERT: l 99 PHE cc_start: 0.7152 (m-80) cc_final: 0.6451 (m-80) outliers start: 48 outliers final: 33 residues processed: 329 average time/residue: 0.2846 time to fit residues: 136.0474 Evaluate side-chains 299 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 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 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 52 LEU 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 52 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: 0.1980 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 423 GLN A 149 GLN ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN h 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.105188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.081020 restraints weight = 37979.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084381 restraints weight = 20097.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086625 restraints weight = 14057.870| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15642 Z= 0.162 Angle : 0.737 10.691 21390 Z= 0.350 Chirality : 0.044 0.266 2604 Planarity : 0.004 0.038 2514 Dihedral : 7.467 59.619 3903 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.70 % Allowed : 13.19 % Favored : 83.11 % 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: 1.11 (0.28), residues: 375 sheet: 0.18 (0.25), residues: 423 loop : -0.84 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP H 52 HIS 0.005 0.001 HIS B 230 PHE 0.015 0.001 PHE K 76 TYR 0.023 0.001 TYR a 419 ARG 0.006 0.000 ARG a 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 33) link_NAG-ASN : angle 1.79084 ( 99) link_ALPHA1-6 : bond 0.00881 ( 6) link_ALPHA1-6 : angle 1.57265 ( 18) link_BETA1-4 : bond 0.00797 ( 45) link_BETA1-4 : angle 2.56164 ( 135) link_ALPHA1-2 : bond 0.00025 ( 3) link_ALPHA1-2 : angle 2.00992 ( 9) link_ALPHA1-3 : bond 0.01687 ( 12) link_ALPHA1-3 : angle 3.33045 ( 36) hydrogen bonds : bond 0.03872 ( 552) hydrogen bonds : angle 5.16449 ( 1566) SS BOND : bond 0.00607 ( 27) SS BOND : angle 2.11123 ( 54) covalent geometry : bond 0.00363 (15516) covalent geometry : angle 0.67913 (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 347 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8838 (mmmt) REVERT: C 156 ASP cc_start: 0.7993 (t70) cc_final: 0.6896 (t0) REVERT: C 161 LYS cc_start: 0.8747 (ttmt) cc_final: 0.8285 (ttpp) REVERT: C 194 MET cc_start: 0.9083 (tpp) cc_final: 0.8176 (ttp) REVERT: C 214 MET cc_start: 0.7991 (ptp) cc_final: 0.7652 (ptp) REVERT: C 244 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8125 (tp) REVERT: B 116 LYS cc_start: 0.9178 (mmtm) cc_final: 0.8927 (mmmt) REVERT: B 156 ASP cc_start: 0.8005 (t70) cc_final: 0.7640 (t0) REVERT: B 161 LYS cc_start: 0.8572 (ttmt) cc_final: 0.7934 (tptt) REVERT: c 282 ARG cc_start: 0.8586 (tpt90) cc_final: 0.7958 (tpm170) REVERT: c 311 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7912 (t0) REVERT: c 326 LEU cc_start: 0.8185 (mp) cc_final: 0.7976 (mp) REVERT: c 415 LEU cc_start: 0.8547 (mt) cc_final: 0.8346 (pp) REVERT: c 420 MET cc_start: 0.7443 (mmt) cc_final: 0.6558 (tpt) REVERT: A 67 GLU cc_start: 0.7627 (tt0) cc_final: 0.7255 (tm-30) REVERT: A 116 LYS cc_start: 0.9153 (mmtm) cc_final: 0.8895 (mmmt) REVERT: A 161 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8416 (ttpp) REVERT: A 194 MET cc_start: 0.8876 (tpp) cc_final: 0.8672 (tpp) REVERT: b 284 MET cc_start: 0.8163 (mtm) cc_final: 0.7624 (mtm) REVERT: b 303 GLU cc_start: 0.7243 (tp30) cc_final: 0.6790 (tp30) REVERT: b 311 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8071 (t0) REVERT: b 326 LEU cc_start: 0.8410 (mp) cc_final: 0.7833 (tp) REVERT: b 420 MET cc_start: 0.7781 (mmt) cc_final: 0.7147 (tpt) REVERT: a 282 ARG cc_start: 0.8422 (tpt90) cc_final: 0.7829 (tpm170) REVERT: a 284 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8088 (mtp) REVERT: a 311 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7586 (t0) REVERT: a 348 GLN cc_start: 0.4917 (mt0) cc_final: 0.4154 (tt0) REVERT: a 410 MET cc_start: 0.7947 (mtp) cc_final: 0.7613 (ttm) REVERT: a 419 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5332 (t80) REVERT: a 420 MET cc_start: 0.8025 (mmt) cc_final: 0.7364 (tpt) REVERT: H 5 GLN cc_start: 0.7139 (tp40) cc_final: 0.6716 (tp-100) REVERT: H 43 ARG cc_start: 0.8489 (ttp-170) cc_final: 0.7998 (mtm110) REVERT: H 51 GLU cc_start: 0.7629 (tt0) cc_final: 0.7358 (tt0) REVERT: H 53 ILE cc_start: 0.8391 (mt) cc_final: 0.7947 (mt) REVERT: H 90 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8175 (mtpp) REVERT: H 98 ASP cc_start: 0.7413 (m-30) cc_final: 0.6997 (m-30) REVERT: L 17 GLU cc_start: 0.7350 (mp0) cc_final: 0.7010 (mp0) REVERT: L 18 ARG cc_start: 0.8399 (ttm170) cc_final: 0.7565 (ttp80) REVERT: L 90 THR cc_start: 0.8636 (m) cc_final: 0.8434 (p) REVERT: L 94 LEU cc_start: 0.7739 (tp) cc_final: 0.7063 (tt) REVERT: L 99 PHE cc_start: 0.7160 (m-80) cc_final: 0.6390 (m-80) REVERT: J 5 GLN cc_start: 0.7162 (tp40) cc_final: 0.6812 (tp-100) REVERT: J 43 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.8027 (mtm110) REVERT: J 52 TRP cc_start: 0.7958 (t60) cc_final: 0.7274 (t60) REVERT: J 98 ASP cc_start: 0.6954 (m-30) cc_final: 0.6601 (m-30) REVERT: K 5 THR cc_start: 0.7726 (m) cc_final: 0.7519 (p) REVERT: K 17 GLU cc_start: 0.7842 (mp0) cc_final: 0.6902 (mp0) REVERT: K 90 THR cc_start: 0.8719 (m) cc_final: 0.8452 (p) REVERT: K 94 LEU cc_start: 0.7691 (tp) cc_final: 0.7266 (tt) REVERT: K 99 PHE cc_start: 0.7483 (m-80) cc_final: 0.6965 (m-80) REVERT: K 102 TYR cc_start: 0.7985 (m-80) cc_final: 0.7738 (m-80) REVERT: h 5 GLN cc_start: 0.6783 (tp40) cc_final: 0.6416 (tp-100) REVERT: h 43 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7973 (mtm110) REVERT: h 53 ILE cc_start: 0.8349 (mt) cc_final: 0.7836 (mt) REVERT: h 85 ASN cc_start: 0.7263 (p0) cc_final: 0.6996 (p0) REVERT: h 87 PHE cc_start: 0.8393 (p90) cc_final: 0.7912 (p90) REVERT: h 98 ASP cc_start: 0.6854 (m-30) cc_final: 0.6499 (m-30) REVERT: l 17 GLU cc_start: 0.7770 (mp0) cc_final: 0.7423 (mp0) REVERT: l 90 THR cc_start: 0.8628 (m) cc_final: 0.8250 (p) REVERT: l 94 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7497 (tt) REVERT: l 99 PHE cc_start: 0.7272 (m-80) cc_final: 0.6515 (m-80) outliers start: 57 outliers final: 36 residues processed: 321 average time/residue: 0.2779 time to fit residues: 129.1283 Evaluate side-chains 303 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 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 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 20 THR 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 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 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: 0.0770 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.112081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086452 restraints weight = 37648.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.089812 restraints weight = 20435.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.092039 restraints weight = 14661.324| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15642 Z= 0.137 Angle : 0.715 10.141 21390 Z= 0.337 Chirality : 0.043 0.261 2604 Planarity : 0.004 0.049 2514 Dihedral : 7.002 59.309 3903 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.51 % Allowed : 13.84 % Favored : 82.65 % 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: -0.17 (0.21), residues: 1731 helix: 1.26 (0.28), residues: 375 sheet: 0.20 (0.25), residues: 426 loop : -0.84 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP H 52 HIS 0.006 0.001 HIS a 305 PHE 0.021 0.001 PHE J 87 TYR 0.019 0.001 TYR h 110 ARG 0.010 0.000 ARG l 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 33) link_NAG-ASN : angle 1.65169 ( 99) link_ALPHA1-6 : bond 0.00993 ( 6) link_ALPHA1-6 : angle 1.52609 ( 18) link_BETA1-4 : bond 0.00792 ( 45) link_BETA1-4 : angle 2.44018 ( 135) link_ALPHA1-2 : bond 0.00036 ( 3) link_ALPHA1-2 : angle 2.05378 ( 9) link_ALPHA1-3 : bond 0.01590 ( 12) link_ALPHA1-3 : angle 3.25529 ( 36) hydrogen bonds : bond 0.03609 ( 552) hydrogen bonds : angle 5.03893 ( 1566) SS BOND : bond 0.00551 ( 27) SS BOND : angle 1.80385 ( 54) covalent geometry : bond 0.00299 (15516) covalent geometry : angle 0.66216 (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 336 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.9147 (mmtm) cc_final: 0.8841 (mmmt) REVERT: C 156 ASP cc_start: 0.7964 (t70) cc_final: 0.6883 (t0) REVERT: C 161 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8286 (ttpp) REVERT: C 194 MET cc_start: 0.9045 (tpp) cc_final: 0.8245 (ttp) REVERT: C 214 MET cc_start: 0.7924 (ptp) cc_final: 0.7625 (ptp) REVERT: B 116 LYS cc_start: 0.9180 (mmtm) cc_final: 0.8929 (mmmt) REVERT: B 156 ASP cc_start: 0.7901 (t70) cc_final: 0.7526 (t0) REVERT: B 161 LYS cc_start: 0.8554 (ttmt) cc_final: 0.7927 (tptt) REVERT: c 282 ARG cc_start: 0.8527 (tpt90) cc_final: 0.7961 (tpm170) REVERT: c 303 GLU cc_start: 0.6534 (tp30) cc_final: 0.5809 (tp30) REVERT: c 311 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7915 (t0) REVERT: c 415 LEU cc_start: 0.8568 (mt) cc_final: 0.8367 (pp) REVERT: c 420 MET cc_start: 0.7481 (mmt) cc_final: 0.6847 (tpt) REVERT: A 116 LYS cc_start: 0.9147 (mmtm) cc_final: 0.8908 (mmmt) REVERT: A 161 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8479 (ttpp) REVERT: b 303 GLU cc_start: 0.7213 (tp30) cc_final: 0.6973 (tp30) REVERT: b 311 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8146 (t0) REVERT: b 332 MET cc_start: 0.7819 (tpp) cc_final: 0.7275 (tpp) REVERT: b 420 MET cc_start: 0.7760 (mmt) cc_final: 0.7134 (tpt) REVERT: a 282 ARG cc_start: 0.8432 (tpt90) cc_final: 0.7866 (tpm170) REVERT: a 284 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8230 (mtp) REVERT: a 311 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7676 (t70) REVERT: a 332 MET cc_start: 0.7886 (tpp) cc_final: 0.7215 (tpp) REVERT: a 348 GLN cc_start: 0.4924 (mt0) cc_final: 0.4195 (tt0) REVERT: a 410 MET cc_start: 0.8029 (mtp) cc_final: 0.7636 (ttm) REVERT: a 420 MET cc_start: 0.8049 (mmt) cc_final: 0.7648 (tpt) REVERT: a 423 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: H 5 GLN cc_start: 0.7357 (tp40) cc_final: 0.6899 (tp-100) REVERT: H 19 LEU cc_start: 0.7795 (tt) cc_final: 0.7526 (tt) REVERT: H 21 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6791 (mm) REVERT: H 43 ARG cc_start: 0.8560 (ttp-170) cc_final: 0.8192 (mtm110) REVERT: H 51 GLU cc_start: 0.7621 (tt0) cc_final: 0.7418 (tt0) REVERT: H 53 ILE cc_start: 0.8391 (mt) cc_final: 0.7941 (mt) REVERT: H 90 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8272 (mtpp) REVERT: H 98 ASP cc_start: 0.7308 (m-30) cc_final: 0.6883 (m-30) REVERT: L 17 GLU cc_start: 0.7450 (mp0) cc_final: 0.7122 (mp0) REVERT: L 18 ARG cc_start: 0.8489 (ttm170) cc_final: 0.7579 (ttp80) REVERT: L 94 LEU cc_start: 0.7761 (tp) cc_final: 0.7113 (tt) REVERT: L 99 PHE cc_start: 0.7198 (m-80) cc_final: 0.6462 (m-80) REVERT: J 5 GLN cc_start: 0.7083 (tp40) cc_final: 0.6678 (tp-100) REVERT: J 30 PHE cc_start: 0.8282 (t80) cc_final: 0.8009 (t80) REVERT: J 43 ARG cc_start: 0.8473 (ttp-170) cc_final: 0.8182 (mtm110) REVERT: J 52 TRP cc_start: 0.8020 (t60) cc_final: 0.7648 (t60) REVERT: J 98 ASP cc_start: 0.6957 (m-30) cc_final: 0.6548 (m-30) REVERT: K 17 GLU cc_start: 0.8091 (mp0) cc_final: 0.7218 (mp0) REVERT: K 42 TYR cc_start: 0.8592 (m-80) cc_final: 0.7965 (m-80) REVERT: K 90 THR cc_start: 0.8707 (m) cc_final: 0.8483 (p) REVERT: K 94 LEU cc_start: 0.7716 (tp) cc_final: 0.7291 (tt) REVERT: K 99 PHE cc_start: 0.7530 (m-80) cc_final: 0.7001 (m-80) REVERT: h 5 GLN cc_start: 0.6836 (tp40) cc_final: 0.6512 (tp-100) REVERT: h 43 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8112 (mtm110) REVERT: h 52 TRP cc_start: 0.8045 (t60) cc_final: 0.7664 (t60) REVERT: h 53 ILE cc_start: 0.8484 (mt) cc_final: 0.7911 (mt) REVERT: h 85 ASN cc_start: 0.7192 (p0) cc_final: 0.6891 (p0) REVERT: h 87 PHE cc_start: 0.8406 (p90) cc_final: 0.8041 (p90) REVERT: h 98 ASP cc_start: 0.6800 (m-30) cc_final: 0.6399 (m-30) REVERT: l 17 GLU cc_start: 0.7894 (mp0) cc_final: 0.7537 (mp0) REVERT: l 90 THR cc_start: 0.8718 (m) cc_final: 0.8355 (p) REVERT: l 94 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7427 (tt) REVERT: l 99 PHE cc_start: 0.7181 (m-80) cc_final: 0.6482 (m-80) outliers start: 54 outliers final: 31 residues processed: 315 average time/residue: 0.2949 time to fit residues: 135.5446 Evaluate side-chains 287 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 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 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain a residue 423 GLN Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 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: 0.6980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.109110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083649 restraints weight = 38374.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087006 restraints weight = 20885.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089219 restraints weight = 14905.337| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15642 Z= 0.141 Angle : 0.716 10.462 21390 Z= 0.339 Chirality : 0.043 0.254 2604 Planarity : 0.004 0.043 2514 Dihedral : 6.636 54.365 3903 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.12 % Allowed : 14.88 % 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: -0.22 (0.21), residues: 1731 helix: 1.24 (0.29), residues: 375 sheet: 0.21 (0.25), residues: 426 loop : -0.89 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 52 HIS 0.006 0.001 HIS a 305 PHE 0.022 0.001 PHE J 87 TYR 0.031 0.001 TYR c 419 ARG 0.008 0.000 ARG l 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 33) link_NAG-ASN : angle 1.56286 ( 99) link_ALPHA1-6 : bond 0.01069 ( 6) link_ALPHA1-6 : angle 1.51493 ( 18) link_BETA1-4 : bond 0.00773 ( 45) link_BETA1-4 : angle 2.36254 ( 135) link_ALPHA1-2 : bond 0.00044 ( 3) link_ALPHA1-2 : angle 2.04428 ( 9) link_ALPHA1-3 : bond 0.01539 ( 12) link_ALPHA1-3 : angle 3.22305 ( 36) hydrogen bonds : bond 0.03614 ( 552) hydrogen bonds : angle 4.95227 ( 1566) SS BOND : bond 0.00593 ( 27) SS BOND : angle 1.76689 ( 54) covalent geometry : bond 0.00309 (15516) covalent geometry : angle 0.66699 (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 319 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 271 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7140 (mp0) cc_final: 0.6907 (mp0) REVERT: C 75 MET cc_start: 0.8457 (mtm) cc_final: 0.8216 (mtm) REVERT: C 156 ASP cc_start: 0.7921 (t70) cc_final: 0.6836 (t0) REVERT: C 161 LYS cc_start: 0.8757 (ttmt) cc_final: 0.8333 (ttpp) REVERT: C 194 MET cc_start: 0.9027 (tpp) cc_final: 0.8273 (ttp) REVERT: C 214 MET cc_start: 0.7919 (ptp) cc_final: 0.7668 (ptp) REVERT: B 116 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8924 (mmmt) REVERT: B 151 GLU cc_start: 0.8197 (pm20) cc_final: 0.7882 (pm20) REVERT: B 156 ASP cc_start: 0.7945 (t70) cc_final: 0.7563 (t0) REVERT: B 161 LYS cc_start: 0.8569 (ttmt) cc_final: 0.7945 (tptt) REVERT: B 218 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8388 (mm-40) REVERT: c 282 ARG cc_start: 0.8562 (tpt90) cc_final: 0.8009 (tpm170) REVERT: c 303 GLU cc_start: 0.6646 (tp30) cc_final: 0.5907 (tp30) REVERT: c 311 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8003 (t0) REVERT: c 326 LEU cc_start: 0.8297 (mp) cc_final: 0.7919 (tp) REVERT: c 348 GLN cc_start: 0.5025 (mt0) cc_final: 0.4353 (tt0) REVERT: c 419 TYR cc_start: 0.7132 (t80) cc_final: 0.6844 (t80) REVERT: c 420 MET cc_start: 0.7603 (mmt) cc_final: 0.6834 (tpt) REVERT: A 116 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8919 (mmmt) REVERT: A 161 LYS cc_start: 0.8821 (ttmt) cc_final: 0.8416 (ttpp) REVERT: A 194 MET cc_start: 0.8720 (tpp) cc_final: 0.8109 (ttm) REVERT: b 284 MET cc_start: 0.8323 (mtm) cc_final: 0.7627 (mtm) REVERT: b 303 GLU cc_start: 0.7239 (tp30) cc_final: 0.7007 (tp30) REVERT: b 311 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8133 (t0) REVERT: b 332 MET cc_start: 0.7782 (tpp) cc_final: 0.7382 (tpp) REVERT: b 420 MET cc_start: 0.7675 (mmt) cc_final: 0.7060 (tpt) REVERT: a 282 ARG cc_start: 0.8460 (tpt90) cc_final: 0.8040 (tpt170) REVERT: a 284 MET cc_start: 0.8460 (mtp) cc_final: 0.8179 (mtp) REVERT: a 311 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7729 (t70) REVERT: a 348 GLN cc_start: 0.4962 (mt0) cc_final: 0.3993 (tt0) REVERT: a 410 MET cc_start: 0.8051 (mtp) cc_final: 0.7582 (ttm) REVERT: a 419 TYR cc_start: 0.6085 (OUTLIER) cc_final: 0.5373 (t80) REVERT: a 420 MET cc_start: 0.8007 (mmt) cc_final: 0.7429 (tpt) REVERT: H 19 LEU cc_start: 0.7849 (tt) cc_final: 0.7599 (tt) REVERT: H 21 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6720 (mm) REVERT: H 43 ARG cc_start: 0.8487 (ttp-170) cc_final: 0.8148 (mtm110) REVERT: H 53 ILE cc_start: 0.8469 (mt) cc_final: 0.8028 (mt) REVERT: H 98 ASP cc_start: 0.7358 (m-30) cc_final: 0.6947 (m-30) REVERT: L 17 GLU cc_start: 0.7509 (mp0) cc_final: 0.7172 (mp0) REVERT: L 18 ARG cc_start: 0.8511 (ttm170) cc_final: 0.7554 (ttp80) REVERT: L 94 LEU cc_start: 0.7788 (tp) cc_final: 0.7160 (tt) REVERT: L 99 PHE cc_start: 0.7527 (m-80) cc_final: 0.6787 (m-80) REVERT: J 5 GLN cc_start: 0.7083 (tp40) cc_final: 0.6677 (tp-100) REVERT: J 30 PHE cc_start: 0.8341 (t80) cc_final: 0.8118 (t80) REVERT: J 43 ARG cc_start: 0.8400 (ttp-170) cc_final: 0.8031 (mtm110) REVERT: J 52 TRP cc_start: 0.8033 (t60) cc_final: 0.7593 (t60) REVERT: J 98 ASP cc_start: 0.7063 (m-30) cc_final: 0.6665 (m-30) REVERT: K 17 GLU cc_start: 0.8210 (mp0) cc_final: 0.7376 (mp0) REVERT: K 42 TYR cc_start: 0.8577 (m-80) cc_final: 0.7957 (m-80) REVERT: K 90 THR cc_start: 0.8751 (m) cc_final: 0.8538 (p) REVERT: K 94 LEU cc_start: 0.7731 (tp) cc_final: 0.7298 (tt) REVERT: K 99 PHE cc_start: 0.7510 (m-80) cc_final: 0.7026 (m-80) REVERT: h 5 GLN cc_start: 0.6893 (tp40) cc_final: 0.6521 (tp-100) REVERT: h 43 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8172 (mtm110) REVERT: h 53 ILE cc_start: 0.8489 (mt) cc_final: 0.7996 (mt) REVERT: h 87 PHE cc_start: 0.8467 (p90) cc_final: 0.8130 (p90) REVERT: h 98 ASP cc_start: 0.6635 (m-30) cc_final: 0.6213 (m-30) REVERT: l 17 GLU cc_start: 0.7916 (mp0) cc_final: 0.7565 (mp0) REVERT: l 90 THR cc_start: 0.8766 (m) cc_final: 0.8399 (p) REVERT: l 99 PHE cc_start: 0.7259 (m-80) cc_final: 0.6607 (m-80) outliers start: 48 outliers final: 33 residues processed: 297 average time/residue: 0.2782 time to fit residues: 119.4919 Evaluate side-chains 288 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 388 VAL Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 311 ASP 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 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 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 52 LEU 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 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: 2.9990 chunk 127 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** K 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.108270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084135 restraints weight = 37433.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087438 restraints weight = 20578.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089596 restraints weight = 14752.544| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15642 Z= 0.141 Angle : 0.718 12.566 21390 Z= 0.335 Chirality : 0.043 0.250 2604 Planarity : 0.004 0.048 2514 Dihedral : 6.416 43.756 3903 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.92 % Allowed : 15.59 % Favored : 81.48 % 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: -0.23 (0.21), residues: 1731 helix: 1.23 (0.29), residues: 375 sheet: 0.21 (0.25), residues: 426 loop : -0.91 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 52 HIS 0.004 0.001 HIS B 230 PHE 0.022 0.001 PHE J 87 TYR 0.036 0.001 TYR c 419 ARG 0.012 0.000 ARG L 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 33) link_NAG-ASN : angle 1.53658 ( 99) link_ALPHA1-6 : bond 0.01076 ( 6) link_ALPHA1-6 : angle 1.52292 ( 18) link_BETA1-4 : bond 0.00761 ( 45) link_BETA1-4 : angle 2.31089 ( 135) link_ALPHA1-2 : bond 0.00070 ( 3) link_ALPHA1-2 : angle 2.04764 ( 9) link_ALPHA1-3 : bond 0.01485 ( 12) link_ALPHA1-3 : angle 3.25153 ( 36) hydrogen bonds : bond 0.03506 ( 552) hydrogen bonds : angle 4.88367 ( 1566) SS BOND : bond 0.00737 ( 27) SS BOND : angle 1.53083 ( 54) covalent geometry : bond 0.00309 (15516) covalent geometry : angle 0.67150 (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 309 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7189 (mp0) cc_final: 0.6895 (mp0) REVERT: C 156 ASP cc_start: 0.7904 (t70) cc_final: 0.7018 (t0) REVERT: C 161 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8380 (ttpp) REVERT: C 194 MET cc_start: 0.9017 (tpp) cc_final: 0.8292 (ttp) REVERT: B 116 LYS cc_start: 0.9139 (mmtm) cc_final: 0.8919 (mmmt) REVERT: B 156 ASP cc_start: 0.7934 (t70) cc_final: 0.7552 (t0) REVERT: B 161 LYS cc_start: 0.8576 (ttmt) cc_final: 0.7961 (tptt) REVERT: B 218 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8404 (mm-40) REVERT: c 282 ARG cc_start: 0.8604 (tpt90) cc_final: 0.8086 (tpm170) REVERT: c 303 GLU cc_start: 0.6716 (tp30) cc_final: 0.6222 (tp30) REVERT: c 311 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7980 (t0) REVERT: c 326 LEU cc_start: 0.8302 (mp) cc_final: 0.7895 (tp) REVERT: c 348 GLN cc_start: 0.4881 (mt0) cc_final: 0.4243 (tt0) REVERT: c 420 MET cc_start: 0.7468 (mmt) cc_final: 0.6719 (tpt) REVERT: b 284 MET cc_start: 0.8351 (mtm) cc_final: 0.7691 (mtm) REVERT: b 311 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8142 (t0) REVERT: b 332 MET cc_start: 0.7774 (tpp) cc_final: 0.7305 (tpp) REVERT: b 351 MET cc_start: 0.9132 (tpp) cc_final: 0.8881 (mmm) REVERT: b 420 MET cc_start: 0.7671 (mmt) cc_final: 0.7050 (tpt) REVERT: a 282 ARG cc_start: 0.8493 (tpt90) cc_final: 0.8071 (tpt170) REVERT: a 284 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8198 (mtp) REVERT: a 311 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7783 (t0) REVERT: a 326 LEU cc_start: 0.8552 (mt) cc_final: 0.8208 (mt) REVERT: a 332 MET cc_start: 0.7684 (tpp) cc_final: 0.7014 (tpp) REVERT: a 348 GLN cc_start: 0.4860 (mt0) cc_final: 0.4071 (tt0) REVERT: a 410 MET cc_start: 0.8086 (mtp) cc_final: 0.7568 (ttm) REVERT: a 419 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.5320 (t80) REVERT: a 420 MET cc_start: 0.7906 (mmt) cc_final: 0.7392 (tpt) REVERT: H 21 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6924 (mm) REVERT: H 43 ARG cc_start: 0.8464 (ttp-170) cc_final: 0.8176 (mtm110) REVERT: H 53 ILE cc_start: 0.8427 (mt) cc_final: 0.7987 (mt) REVERT: H 98 ASP cc_start: 0.7412 (m-30) cc_final: 0.6984 (m-30) REVERT: L 17 GLU cc_start: 0.7527 (mp0) cc_final: 0.7194 (mp0) REVERT: L 18 ARG cc_start: 0.8521 (ttm170) cc_final: 0.7567 (ttp80) REVERT: L 94 LEU cc_start: 0.7781 (tp) cc_final: 0.7131 (tt) REVERT: L 99 PHE cc_start: 0.7517 (m-80) cc_final: 0.6663 (m-80) REVERT: J 5 GLN cc_start: 0.7044 (tp40) cc_final: 0.6689 (tp-100) REVERT: J 43 ARG cc_start: 0.8167 (ttp-170) cc_final: 0.7640 (mtm110) REVERT: J 52 TRP cc_start: 0.7948 (t60) cc_final: 0.7439 (t60) REVERT: J 98 ASP cc_start: 0.7154 (m-30) cc_final: 0.6754 (m-30) REVERT: K 17 GLU cc_start: 0.8282 (mp0) cc_final: 0.7403 (mp0) REVERT: K 42 TYR cc_start: 0.8484 (m-80) cc_final: 0.7971 (m-80) REVERT: K 90 THR cc_start: 0.8801 (m) cc_final: 0.8579 (p) REVERT: K 94 LEU cc_start: 0.7589 (tp) cc_final: 0.7161 (tt) REVERT: K 99 PHE cc_start: 0.7478 (m-80) cc_final: 0.6958 (m-80) REVERT: h 5 GLN cc_start: 0.6972 (tp40) cc_final: 0.6605 (tp-100) REVERT: h 43 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8147 (mtm110) REVERT: h 52 TRP cc_start: 0.8025 (t60) cc_final: 0.7637 (t60) REVERT: h 53 ILE cc_start: 0.8524 (mt) cc_final: 0.7952 (mt) REVERT: h 85 ASN cc_start: 0.7926 (p0) cc_final: 0.7276 (p0) REVERT: h 87 PHE cc_start: 0.8469 (p90) cc_final: 0.8146 (p90) REVERT: h 98 ASP cc_start: 0.6640 (m-30) cc_final: 0.6167 (m-30) REVERT: l 17 GLU cc_start: 0.7879 (mp0) cc_final: 0.7519 (mp0) REVERT: l 90 THR cc_start: 0.8776 (m) cc_final: 0.8420 (p) outliers start: 45 outliers final: 33 residues processed: 284 average time/residue: 0.2779 time to fit residues: 115.1681 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 : 1.584 ------------------------------------------------------------------------------- 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 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 125 LYS 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 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 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 39 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 150 optimal weight: 0.0050 chunk 144 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN L 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.108688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.084504 restraints weight = 37578.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.087822 restraints weight = 20735.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090003 restraints weight = 14826.033| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15642 Z= 0.133 Angle : 0.704 9.962 21390 Z= 0.331 Chirality : 0.042 0.248 2604 Planarity : 0.004 0.055 2514 Dihedral : 6.189 35.686 3903 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.73 % Allowed : 16.24 % Favored : 81.03 % 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 (0.21), residues: 1731 helix: 1.30 (0.29), residues: 375 sheet: 0.26 (0.26), residues: 423 loop : -0.89 (0.21), residues: 933 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 0.024 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 0.00240 ( 33) link_NAG-ASN : angle 1.49321 ( 99) link_ALPHA1-6 : bond 0.01120 ( 6) link_ALPHA1-6 : angle 1.49395 ( 18) link_BETA1-4 : bond 0.00762 ( 45) link_BETA1-4 : angle 2.25775 ( 135) link_ALPHA1-2 : bond 0.00067 ( 3) link_ALPHA1-2 : angle 2.05606 ( 9) link_ALPHA1-3 : bond 0.01454 ( 12) link_ALPHA1-3 : angle 3.24014 ( 36) hydrogen bonds : bond 0.03397 ( 552) hydrogen bonds : angle 4.83645 ( 1566) SS BOND : bond 0.00562 ( 27) SS BOND : angle 1.46785 ( 54) covalent geometry : bond 0.00294 (15516) covalent geometry : angle 0.65891 (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 312 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7096 (mp0) cc_final: 0.6845 (mp0) REVERT: C 156 ASP cc_start: 0.7933 (t70) cc_final: 0.7079 (t0) REVERT: C 161 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8349 (ttpp) REVERT: C 194 MET cc_start: 0.8992 (tpp) cc_final: 0.8279 (ttp) REVERT: B 67 GLU cc_start: 0.7251 (tt0) cc_final: 0.7007 (tm-30) REVERT: B 116 LYS cc_start: 0.9094 (mmtm) cc_final: 0.8882 (mmmt) REVERT: B 156 ASP cc_start: 0.7958 (t70) cc_final: 0.7572 (t0) REVERT: B 161 LYS cc_start: 0.8581 (ttmt) cc_final: 0.7967 (tptt) REVERT: B 218 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8394 (mm-40) REVERT: c 282 ARG cc_start: 0.8627 (tpt90) cc_final: 0.8128 (tpm170) REVERT: c 303 GLU cc_start: 0.6727 (tp30) cc_final: 0.6261 (tp30) REVERT: c 311 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7952 (t0) REVERT: c 326 LEU cc_start: 0.8309 (mp) cc_final: 0.7921 (tp) REVERT: c 348 GLN cc_start: 0.4855 (mt0) cc_final: 0.4295 (tt0) REVERT: c 420 MET cc_start: 0.7486 (mmt) cc_final: 0.6548 (tpt) REVERT: A 151 GLU cc_start: 0.8059 (pm20) cc_final: 0.7767 (pt0) REVERT: A 194 MET cc_start: 0.8664 (tpp) cc_final: 0.8108 (ttm) REVERT: b 284 MET cc_start: 0.8391 (mtm) cc_final: 0.7698 (mtm) REVERT: b 311 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8123 (t0) REVERT: b 332 MET cc_start: 0.7759 (tpp) cc_final: 0.7285 (tpp) REVERT: b 420 MET cc_start: 0.7729 (mmt) cc_final: 0.7189 (tpt) REVERT: a 282 ARG cc_start: 0.8491 (tpt90) cc_final: 0.8100 (tpt170) REVERT: a 284 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8195 (mtp) REVERT: a 311 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7771 (t0) REVERT: a 326 LEU cc_start: 0.8602 (mt) cc_final: 0.8239 (mt) REVERT: a 332 MET cc_start: 0.7639 (tpp) cc_final: 0.6906 (tpp) REVERT: a 348 GLN cc_start: 0.4620 (mt0) cc_final: 0.3897 (tt0) REVERT: a 410 MET cc_start: 0.8053 (mtp) cc_final: 0.7540 (ttm) REVERT: a 419 TYR cc_start: 0.5966 (OUTLIER) cc_final: 0.5704 (t80) REVERT: a 420 MET cc_start: 0.7935 (mmt) cc_final: 0.7537 (tpt) REVERT: H 43 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.8109 (mtm110) REVERT: H 53 ILE cc_start: 0.8383 (mt) cc_final: 0.7941 (mt) REVERT: H 98 ASP cc_start: 0.7401 (m-30) cc_final: 0.6971 (m-30) REVERT: L 17 GLU cc_start: 0.7641 (mp0) cc_final: 0.6803 (mp0) REVERT: L 18 ARG cc_start: 0.8518 (ttm170) cc_final: 0.7573 (ttp80) REVERT: L 94 LEU cc_start: 0.7766 (tp) cc_final: 0.7141 (tt) REVERT: L 99 PHE cc_start: 0.7474 (m-80) cc_final: 0.6660 (m-80) REVERT: L 127 LYS cc_start: 0.7611 (pttt) cc_final: 0.7337 (ptpt) REVERT: J 5 GLN cc_start: 0.7039 (tp40) cc_final: 0.6683 (tp-100) REVERT: J 43 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7888 (mtm110) REVERT: J 52 TRP cc_start: 0.7901 (t60) cc_final: 0.7440 (t60) REVERT: J 98 ASP cc_start: 0.7169 (m-30) cc_final: 0.6795 (m-30) REVERT: J 99 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8229 (p) REVERT: K 17 GLU cc_start: 0.8323 (mp0) cc_final: 0.7465 (mp0) REVERT: K 42 TYR cc_start: 0.8438 (m-80) cc_final: 0.7847 (m-80) REVERT: K 90 THR cc_start: 0.8785 (m) cc_final: 0.8564 (p) REVERT: K 94 LEU cc_start: 0.7455 (tp) cc_final: 0.7005 (tt) REVERT: K 99 PHE cc_start: 0.7408 (m-80) cc_final: 0.6857 (m-80) REVERT: h 5 GLN cc_start: 0.6972 (tp40) cc_final: 0.6588 (tp-100) REVERT: h 43 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8114 (mtm110) REVERT: h 52 TRP cc_start: 0.8020 (t60) cc_final: 0.7584 (t60) REVERT: h 53 ILE cc_start: 0.8455 (mt) cc_final: 0.7882 (mt) REVERT: h 85 ASN cc_start: 0.7797 (p0) cc_final: 0.7084 (p0) REVERT: h 87 PHE cc_start: 0.8441 (p90) cc_final: 0.8120 (p90) REVERT: h 95 THR cc_start: 0.7962 (t) cc_final: 0.7675 (p) REVERT: h 98 ASP cc_start: 0.6509 (m-30) cc_final: 0.6067 (m-30) REVERT: l 17 GLU cc_start: 0.7885 (mp0) cc_final: 0.7542 (mp0) REVERT: l 90 THR cc_start: 0.8766 (m) cc_final: 0.8415 (p) REVERT: l 99 PHE cc_start: 0.7182 (m-80) cc_final: 0.6619 (m-80) outliers start: 42 outliers final: 29 residues processed: 288 average time/residue: 0.2914 time to fit residues: 121.4592 Evaluate side-chains 290 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 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 125 LYS Chi-restraints excluded: chain b residue 311 ASP 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 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 39 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 150 optimal weight: 0.0050 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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** ** 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 = 0.3632 r_free = 0.3632 target = 0.102548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079438 restraints weight = 37738.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.082725 restraints weight = 19496.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084916 restraints weight = 13429.291| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15642 Z= 0.200 Angle : 0.769 11.290 21390 Z= 0.360 Chirality : 0.044 0.239 2604 Planarity : 0.004 0.054 2514 Dihedral : 6.412 35.363 3903 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.66 % Favored : 94.17 % Rotamer: Outliers : 2.47 % Allowed : 16.83 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.21), residues: 1731 helix: 1.21 (0.29), residues: 375 sheet: 0.18 (0.26), residues: 423 loop : -1.00 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 52 HIS 0.004 0.001 HIS A 141 PHE 0.024 0.002 PHE J 87 TYR 0.033 0.002 TYR c 419 ARG 0.012 0.001 ARG L 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 33) link_NAG-ASN : angle 1.70041 ( 99) link_ALPHA1-6 : bond 0.01036 ( 6) link_ALPHA1-6 : angle 1.62518 ( 18) link_BETA1-4 : bond 0.00716 ( 45) link_BETA1-4 : angle 2.33488 ( 135) link_ALPHA1-2 : bond 0.00133 ( 3) link_ALPHA1-2 : angle 2.05532 ( 9) link_ALPHA1-3 : bond 0.01471 ( 12) link_ALPHA1-3 : angle 3.31514 ( 36) hydrogen bonds : bond 0.03933 ( 552) hydrogen bonds : angle 4.99366 ( 1566) SS BOND : bond 0.00710 ( 27) SS BOND : angle 1.62503 ( 54) covalent geometry : bond 0.00456 (15516) covalent geometry : angle 0.72267 (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 288 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 1.578 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: 0.7433 (mp0) cc_final: 0.7090 (mp0) REVERT: C 151 GLU cc_start: 0.8268 (pm20) cc_final: 0.7874 (pm20) REVERT: C 156 ASP cc_start: 0.8068 (t70) cc_final: 0.7099 (t0) REVERT: C 161 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8366 (ttpp) REVERT: C 194 MET cc_start: 0.9082 (tpp) cc_final: 0.8333 (tpp) REVERT: B 116 LYS cc_start: 0.9117 (mmtm) cc_final: 0.8913 (mmmt) REVERT: B 156 ASP cc_start: 0.8083 (t70) cc_final: 0.7378 (t0) REVERT: B 161 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8231 (ttpp) REVERT: B 251 ASP cc_start: 0.7517 (m-30) cc_final: 0.7227 (m-30) REVERT: c 282 ARG cc_start: 0.8633 (tpt90) cc_final: 0.7950 (tpm170) REVERT: c 311 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8073 (t0) REVERT: c 348 GLN cc_start: 0.4895 (mt0) cc_final: 0.4109 (tt0) REVERT: c 419 TYR cc_start: 0.7717 (t80) cc_final: 0.7505 (t80) REVERT: c 420 MET cc_start: 0.7433 (mmt) cc_final: 0.6628 (tpt) REVERT: A 125 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8684 (tppt) REVERT: b 284 MET cc_start: 0.8381 (mtm) cc_final: 0.7668 (mtm) REVERT: b 311 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8062 (t0) REVERT: b 351 MET cc_start: 0.9165 (tpp) cc_final: 0.8867 (mmm) REVERT: b 420 MET cc_start: 0.7722 (mmt) cc_final: 0.7181 (tpt) REVERT: a 284 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8202 (mtp) REVERT: a 311 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7795 (t0) REVERT: a 348 GLN cc_start: 0.4625 (mt0) cc_final: 0.3708 (tt0) REVERT: a 410 MET cc_start: 0.8024 (mtp) cc_final: 0.7461 (ttm) REVERT: a 419 TYR cc_start: 0.5940 (OUTLIER) cc_final: 0.5139 (t80) REVERT: a 420 MET cc_start: 0.7924 (mmt) cc_final: 0.7413 (tpt) REVERT: H 43 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8113 (mtm110) REVERT: H 53 ILE cc_start: 0.8351 (mt) cc_final: 0.7904 (mt) REVERT: H 95 THR cc_start: 0.8143 (t) cc_final: 0.7845 (p) REVERT: H 98 ASP cc_start: 0.7488 (m-30) cc_final: 0.7039 (m-30) REVERT: L 17 GLU cc_start: 0.7562 (mp0) cc_final: 0.7204 (mp0) REVERT: L 18 ARG cc_start: 0.8427 (ttm170) cc_final: 0.7423 (ttp80) REVERT: L 94 LEU cc_start: 0.7666 (tp) cc_final: 0.6998 (tt) REVERT: L 99 PHE cc_start: 0.7586 (m-80) cc_final: 0.6824 (m-80) REVERT: J 5 GLN cc_start: 0.7077 (tp40) cc_final: 0.6736 (tp-100) REVERT: J 52 TRP cc_start: 0.7910 (t60) cc_final: 0.7472 (t60) REVERT: J 98 ASP cc_start: 0.7235 (m-30) cc_final: 0.6809 (m-30) REVERT: K 42 TYR cc_start: 0.8541 (m-80) cc_final: 0.7893 (m-80) REVERT: K 90 THR cc_start: 0.8794 (m) cc_final: 0.8520 (p) REVERT: K 94 LEU cc_start: 0.7367 (tp) cc_final: 0.6953 (tt) REVERT: K 99 PHE cc_start: 0.7679 (m-80) cc_final: 0.7091 (m-80) REVERT: K 125 GLU cc_start: 0.5558 (tt0) cc_final: 0.5290 (tt0) REVERT: h 5 GLN cc_start: 0.7049 (tp40) cc_final: 0.6650 (tp-100) REVERT: h 43 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8047 (mtm110) REVERT: h 52 TRP cc_start: 0.7965 (t60) cc_final: 0.7501 (t60) REVERT: h 53 ILE cc_start: 0.8323 (mt) cc_final: 0.7684 (mt) REVERT: h 87 PHE cc_start: 0.8545 (p90) cc_final: 0.8058 (p90) REVERT: h 95 THR cc_start: 0.8016 (t) cc_final: 0.7694 (p) REVERT: h 98 ASP cc_start: 0.6608 (m-30) cc_final: 0.6083 (m-30) REVERT: l 17 GLU cc_start: 0.7853 (mp0) cc_final: 0.7496 (mp0) REVERT: l 90 THR cc_start: 0.8690 (m) cc_final: 0.8288 (p) REVERT: l 99 PHE cc_start: 0.7573 (m-80) cc_final: 0.7022 (m-80) outliers start: 38 outliers final: 30 residues processed: 271 average time/residue: 0.2747 time to fit residues: 108.1549 Evaluate side-chains 279 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 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 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 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 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 39 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 8 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 117 optimal weight: 0.0040 chunk 111 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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** ** 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 = 0.3662 r_free = 0.3662 target = 0.104349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081421 restraints weight = 37432.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084821 restraints weight = 19191.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087096 restraints weight = 13118.797| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5809 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= 0.134 Angle : 0.711 9.623 21390 Z= 0.333 Chirality : 0.042 0.249 2604 Planarity : 0.004 0.049 2514 Dihedral : 6.153 36.408 3903 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.08 % Favored : 94.80 % Rotamer: Outliers : 2.47 % Allowed : 17.41 % Favored : 80.12 % 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: 1.38 (0.29), residues: 375 sheet: 0.20 (0.26), residues: 420 loop : -0.99 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 52 HIS 0.007 0.001 HIS a 305 PHE 0.025 0.001 PHE J 87 TYR 0.034 0.001 TYR c 419 ARG 0.011 0.000 ARG L 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 33) link_NAG-ASN : angle 1.52479 ( 99) link_ALPHA1-6 : bond 0.01126 ( 6) link_ALPHA1-6 : angle 1.54286 ( 18) link_BETA1-4 : bond 0.00761 ( 45) link_BETA1-4 : angle 2.20955 ( 135) link_ALPHA1-2 : bond 0.00127 ( 3) link_ALPHA1-2 : angle 2.13595 ( 9) link_ALPHA1-3 : bond 0.01436 ( 12) link_ALPHA1-3 : angle 3.23615 ( 36) hydrogen bonds : bond 0.03457 ( 552) hydrogen bonds : angle 4.89794 ( 1566) SS BOND : bond 0.00600 ( 27) SS BOND : angle 1.46037 ( 54) covalent geometry : bond 0.00296 (15516) covalent geometry : angle 0.66694 (21039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4874.85 seconds wall clock time: 86 minutes 54.21 seconds (5214.21 seconds total)