Starting phenix.real_space_refine on Tue Dec 31 09:23:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejh_28182/12_2024/8ejh_28182.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejh_28182/12_2024/8ejh_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_28182/12_2024/8ejh_28182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejh_28182/12_2024/8ejh_28182.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejh_28182/12_2024/8ejh_28182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejh_28182/12_2024/8ejh_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-5532/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: 9.88, per 1000 atoms: 0.65 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: 5.61 Conformation dependent library (CDL) restraints added in 1.7 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: 1.82 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: 5.05 Time building geometry restraints manager: 6.24 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: 0.00 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.130 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.120 ------------------------------------------------------------------------------- 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 : 0.021 0.117 15516 Z= 1.360 Angle : 1.825 10.041 21039 Z= 1.158 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 *********************** 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 : 1.829 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: 0.3297 time to fit residues: 246.3419 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 : 1.688 ------------------------------------------------------------------------------- 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: 3.9990 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: 1.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 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 15516 Z= 0.258 Angle : 0.831 9.030 21039 Z= 0.419 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 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 362 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.8579 (tpp) cc_final: 0.7861 (tpp) REVERT: B 82 MET cc_start: 0.8774 (ptp) cc_final: 0.8568 (ptp) REVERT: B 194 MET cc_start: 0.8654 (tpp) cc_final: 0.8297 (tpp) REVERT: c 419 TYR cc_start: 0.7537 (t80) cc_final: 0.7259 (t80) REVERT: c 420 MET cc_start: 0.7503 (mmt) cc_final: 0.6478 (tpt) REVERT: A 96 MET cc_start: 0.7940 (mmm) cc_final: 0.7735 (mmm) REVERT: A 194 MET cc_start: 0.8625 (tpp) cc_final: 0.8380 (tpp) REVERT: b 306 ASP cc_start: 0.7845 (p0) cc_final: 0.7631 (p0) REVERT: b 414 MET cc_start: 0.8123 (tpp) cc_final: 0.7906 (tpp) REVERT: b 420 MET cc_start: 0.7488 (mmt) cc_final: 0.7018 (tpt) REVERT: b 423 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7671 (mp10) REVERT: a 306 ASP cc_start: 0.7914 (p0) cc_final: 0.7541 (p0) REVERT: a 409 ASN cc_start: 0.8624 (m-40) cc_final: 0.8333 (m110) REVERT: a 414 MET cc_start: 0.8227 (tpp) cc_final: 0.7986 (tpp) REVERT: a 420 MET cc_start: 0.7649 (mmt) cc_final: 0.7049 (tpt) REVERT: H 13 LEU cc_start: 0.7940 (mt) cc_final: 0.7567 (pp) REVERT: H 98 ASP cc_start: 0.8047 (m-30) cc_final: 0.7802 (m-30) REVERT: H 112 TYR cc_start: 0.8200 (p90) cc_final: 0.7833 (p90) REVERT: L 17 GLU cc_start: 0.7981 (mp0) cc_final: 0.7721 (mp0) REVERT: L 18 ARG cc_start: 0.8169 (ttm170) cc_final: 0.7778 (ttp80) REVERT: L 90 THR cc_start: 0.8528 (m) cc_final: 0.8253 (p) REVERT: L 94 LEU cc_start: 0.7727 (tp) cc_final: 0.7478 (tt) REVERT: L 99 PHE cc_start: 0.7217 (m-80) cc_final: 0.6635 (m-80) REVERT: L 128 LYS cc_start: 0.7959 (tmmt) cc_final: 0.7729 (pttm) REVERT: J 43 ARG cc_start: 0.8787 (ttp-170) cc_final: 0.8556 (ttp-170) REVERT: J 52 TRP cc_start: 0.8394 (t60) cc_final: 0.7837 (t60) REVERT: J 98 ASP cc_start: 0.7721 (m-30) cc_final: 0.7477 (m-30) REVERT: K 18 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7729 (ttp80) REVERT: K 99 PHE cc_start: 0.7204 (m-80) cc_final: 0.6864 (m-80) REVERT: h 43 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8670 (ttp80) REVERT: h 87 PHE cc_start: 0.8499 (p90) cc_final: 0.8182 (p90) REVERT: h 98 ASP cc_start: 0.7757 (m-30) cc_final: 0.7547 (m-30) REVERT: l 17 GLU cc_start: 0.8167 (mp0) cc_final: 0.7868 (mp0) REVERT: l 18 ARG cc_start: 0.8409 (ttm170) cc_final: 0.7703 (ttp80) REVERT: l 90 THR cc_start: 0.8428 (m) cc_final: 0.8136 (p) REVERT: l 122 THR cc_start: 0.8291 (p) cc_final: 0.7992 (p) outliers start: 28 outliers final: 18 residues processed: 375 average time/residue: 0.3017 time to fit residues: 161.8939 Evaluate side-chains 296 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 278 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 423 GLN ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15516 Z= 0.295 Angle : 0.786 11.337 21039 Z= 0.384 Chirality : 0.047 0.244 2604 Planarity : 0.004 0.038 2514 Dihedral : 10.711 63.185 3903 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.25 % Allowed : 11.70 % Favored : 85.06 % 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: -0.27 (0.20), residues: 1731 helix: 0.69 (0.28), residues: 375 sheet: 0.18 (0.25), residues: 420 loop : -0.67 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 52 HIS 0.007 0.002 HIS B 230 PHE 0.031 0.002 PHE J 87 TYR 0.025 0.002 TYR a 419 ARG 0.011 0.001 ARG c 282 *********************** 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 353 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 1.757 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: B 194 MET cc_start: 0.8765 (tpp) cc_final: 0.8444 (tpp) REVERT: c 419 TYR cc_start: 0.7513 (t80) cc_final: 0.7210 (t80) REVERT: c 420 MET cc_start: 0.7552 (mmt) cc_final: 0.6531 (tpt) REVERT: A 80 MET cc_start: 0.8428 (mmt) cc_final: 0.8202 (mmt) REVERT: A 194 MET cc_start: 0.8663 (tpp) cc_final: 0.8432 (tpp) REVERT: A 245 LEU cc_start: 0.8368 (tp) cc_final: 0.8082 (tp) REVERT: b 303 GLU cc_start: 0.6400 (tp30) cc_final: 0.6117 (tp30) REVERT: b 306 ASP cc_start: 0.7798 (p0) cc_final: 0.7574 (p0) REVERT: b 332 MET cc_start: 0.6093 (mmm) cc_final: 0.5822 (tpp) REVERT: b 418 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8204 (mt-10) REVERT: b 420 MET cc_start: 0.7902 (mmt) cc_final: 0.7309 (tpt) REVERT: a 306 ASP cc_start: 0.7934 (p0) cc_final: 0.7546 (p0) REVERT: a 420 MET cc_start: 0.8067 (mmt) cc_final: 0.7575 (tpt) REVERT: H 13 LEU cc_start: 0.7969 (mt) cc_final: 0.7643 (pp) REVERT: H 53 ILE cc_start: 0.9016 (mt) cc_final: 0.8775 (mt) REVERT: H 98 ASP cc_start: 0.8109 (m-30) cc_final: 0.7862 (m-30) REVERT: H 108 TYR cc_start: 0.7742 (t80) cc_final: 0.7495 (t80) REVERT: H 112 TYR cc_start: 0.8278 (p90) cc_final: 0.7846 (p90) REVERT: L 18 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7660 (ttp80) REVERT: L 90 THR cc_start: 0.8647 (m) cc_final: 0.8434 (p) REVERT: L 94 LEU cc_start: 0.7887 (tp) cc_final: 0.7548 (tt) REVERT: L 99 PHE cc_start: 0.7226 (m-80) cc_final: 0.6791 (m-80) REVERT: L 122 THR cc_start: 0.7931 (p) cc_final: 0.7706 (p) REVERT: J 5 GLN cc_start: 0.7419 (tp40) cc_final: 0.7116 (tp-100) REVERT: J 52 TRP cc_start: 0.8491 (t60) cc_final: 0.8164 (t60) REVERT: J 98 ASP cc_start: 0.7842 (m-30) cc_final: 0.7478 (m-30) REVERT: K 17 GLU cc_start: 0.8251 (mp0) cc_final: 0.8040 (mp0) REVERT: K 99 PHE cc_start: 0.7458 (m-80) cc_final: 0.7157 (m-80) REVERT: K 122 THR cc_start: 0.8548 (p) cc_final: 0.8224 (p) REVERT: h 87 PHE cc_start: 0.8541 (p90) cc_final: 0.8289 (p90) REVERT: h 98 ASP cc_start: 0.7840 (m-30) cc_final: 0.7611 (m-30) REVERT: l 18 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7512 (ttp80) REVERT: l 90 THR cc_start: 0.8560 (m) cc_final: 0.8346 (p) REVERT: l 99 PHE cc_start: 0.7233 (m-80) cc_final: 0.6766 (m-80) REVERT: l 122 THR cc_start: 0.8357 (p) cc_final: 0.8003 (p) outliers start: 50 outliers final: 28 residues processed: 324 average time/residue: 0.2894 time to fit residues: 136.0751 Evaluate side-chains 282 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 292 CYS Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 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 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 156 optimal weight: 0.0040 chunk 165 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 149 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15516 Z= 0.224 Angle : 0.714 10.711 21039 Z= 0.348 Chirality : 0.045 0.259 2604 Planarity : 0.004 0.035 2514 Dihedral : 8.356 50.662 3903 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.25 % Allowed : 13.13 % Favored : 83.63 % 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: 0.98 (0.28), residues: 375 sheet: 0.21 (0.25), residues: 417 loop : -0.70 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 52 HIS 0.005 0.001 HIS B 230 PHE 0.015 0.001 PHE H 87 TYR 0.028 0.001 TYR b 419 ARG 0.005 0.000 ARG a 282 *********************** 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 340 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 1.722 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 194 MET cc_start: 0.8443 (tpp) cc_final: 0.7783 (tpp) REVERT: B 194 MET cc_start: 0.8698 (tpp) cc_final: 0.8485 (tpp) REVERT: c 420 MET cc_start: 0.7672 (mmt) cc_final: 0.6685 (tpt) REVERT: A 194 MET cc_start: 0.8567 (tpp) cc_final: 0.8348 (tpp) REVERT: A 245 LEU cc_start: 0.8311 (tp) cc_final: 0.8091 (tp) REVERT: b 306 ASP cc_start: 0.7790 (p0) cc_final: 0.7575 (p0) REVERT: b 311 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7783 (t0) REVERT: b 418 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8333 (mt-10) REVERT: b 419 TYR cc_start: 0.7434 (t80) cc_final: 0.7121 (t80) REVERT: b 420 MET cc_start: 0.7824 (mmt) cc_final: 0.7045 (tpt) REVERT: a 306 ASP cc_start: 0.7928 (p0) cc_final: 0.7662 (p0) REVERT: a 311 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7444 (t0) REVERT: a 348 GLN cc_start: 0.5616 (mt0) cc_final: 0.5077 (tt0) REVERT: a 420 MET cc_start: 0.8156 (mmt) cc_final: 0.7526 (tpt) REVERT: H 98 ASP cc_start: 0.8019 (m-30) cc_final: 0.7793 (m-30) REVERT: H 108 TYR cc_start: 0.7699 (t80) cc_final: 0.7478 (t80) REVERT: H 112 TYR cc_start: 0.8207 (p90) cc_final: 0.7761 (p90) REVERT: L 18 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7552 (ttp80) REVERT: L 94 LEU cc_start: 0.7824 (tp) cc_final: 0.7473 (tt) REVERT: L 99 PHE cc_start: 0.7195 (m-80) cc_final: 0.6771 (m-80) REVERT: J 43 ARG cc_start: 0.8834 (ttp-170) cc_final: 0.8520 (mtm110) REVERT: J 52 TRP cc_start: 0.8463 (t60) cc_final: 0.8146 (t60) REVERT: J 98 ASP cc_start: 0.7686 (m-30) cc_final: 0.7373 (m-30) REVERT: K 17 GLU cc_start: 0.8226 (mp0) cc_final: 0.7473 (mp0) REVERT: K 99 PHE cc_start: 0.7324 (m-80) cc_final: 0.6824 (m-80) REVERT: h 13 LEU cc_start: 0.7766 (mt) cc_final: 0.7427 (pp) REVERT: l 18 ARG cc_start: 0.7900 (ttm170) cc_final: 0.7466 (ttp80) REVERT: l 90 THR cc_start: 0.8700 (m) cc_final: 0.8485 (p) REVERT: l 122 THR cc_start: 0.8252 (p) cc_final: 0.7951 (p) outliers start: 50 outliers final: 30 residues processed: 321 average time/residue: 0.2827 time to fit residues: 132.4308 Evaluate side-chains 283 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 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 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 39 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15516 Z= 0.252 Angle : 0.706 10.905 21039 Z= 0.346 Chirality : 0.044 0.263 2604 Planarity : 0.004 0.041 2514 Dihedral : 7.465 47.704 3903 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.44 % Allowed : 13.97 % Favored : 82.59 % 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 (0.20), residues: 1731 helix: 1.12 (0.28), residues: 375 sheet: 0.27 (0.25), residues: 423 loop : -0.86 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 52 HIS 0.005 0.001 HIS a 305 PHE 0.020 0.002 PHE J 87 TYR 0.036 0.001 TYR b 419 ARG 0.005 0.001 ARG a 282 *********************** 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 326 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 287 GLU cc_start: 0.7808 (pp20) cc_final: 0.7606 (pp20) REVERT: c 311 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7429 (t0) REVERT: c 420 MET cc_start: 0.7597 (mmt) cc_final: 0.6680 (tpt) REVERT: A 80 MET cc_start: 0.8529 (mmm) cc_final: 0.8103 (mmt) REVERT: A 194 MET cc_start: 0.8635 (tpp) cc_final: 0.8378 (tpp) REVERT: b 306 ASP cc_start: 0.7818 (p0) cc_final: 0.7537 (p0) REVERT: b 311 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7818 (t0) REVERT: b 418 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8239 (mt-10) REVERT: b 419 TYR cc_start: 0.7189 (t80) cc_final: 0.6930 (t80) REVERT: b 420 MET cc_start: 0.7809 (mmt) cc_final: 0.7101 (tpt) REVERT: a 306 ASP cc_start: 0.7615 (p0) cc_final: 0.7351 (p0) REVERT: a 311 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7058 (t0) REVERT: a 348 GLN cc_start: 0.5729 (mt0) cc_final: 0.5056 (tt0) REVERT: a 410 MET cc_start: 0.8506 (mtp) cc_final: 0.8116 (ttm) REVERT: a 420 MET cc_start: 0.8167 (mmt) cc_final: 0.7672 (tpt) REVERT: H 98 ASP cc_start: 0.8103 (m-30) cc_final: 0.7878 (m-30) REVERT: H 108 TYR cc_start: 0.7743 (t80) cc_final: 0.7493 (t80) REVERT: H 112 TYR cc_start: 0.8245 (p90) cc_final: 0.7835 (p90) REVERT: L 18 ARG cc_start: 0.8357 (ttm170) cc_final: 0.7528 (ttp80) REVERT: L 94 LEU cc_start: 0.7813 (tp) cc_final: 0.7490 (tt) REVERT: L 99 PHE cc_start: 0.7235 (m-80) cc_final: 0.6800 (m-80) REVERT: J 43 ARG cc_start: 0.8850 (ttp-170) cc_final: 0.8559 (mtm110) REVERT: J 52 TRP cc_start: 0.8401 (t60) cc_final: 0.8111 (t60) REVERT: J 98 ASP cc_start: 0.7684 (m-30) cc_final: 0.7335 (m-30) REVERT: K 17 GLU cc_start: 0.8335 (mp0) cc_final: 0.7579 (mp0) REVERT: K 99 PHE cc_start: 0.7420 (m-80) cc_final: 0.6923 (m-80) REVERT: h 13 LEU cc_start: 0.7797 (mt) cc_final: 0.7431 (pp) REVERT: l 99 PHE cc_start: 0.7240 (m-80) cc_final: 0.6767 (m-80) outliers start: 53 outliers final: 34 residues processed: 305 average time/residue: 0.2773 time to fit residues: 123.7455 Evaluate side-chains 276 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN B 158 ASN ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 423 GLN A 149 GLN ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15516 Z= 0.292 Angle : 0.729 10.124 21039 Z= 0.357 Chirality : 0.044 0.262 2604 Planarity : 0.004 0.043 2514 Dihedral : 7.239 55.137 3903 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.45 % Rotamer: Outliers : 3.57 % Allowed : 13.58 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1731 helix: 1.14 (0.28), residues: 375 sheet: 0.15 (0.25), residues: 423 loop : -0.97 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP H 52 HIS 0.005 0.001 HIS B 230 PHE 0.021 0.002 PHE J 87 TYR 0.037 0.002 TYR a 419 ARG 0.006 0.001 ARG b 422 *********************** 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 310 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.7972 (mtm) cc_final: 0.7702 (mtm) REVERT: C 194 MET cc_start: 0.8263 (tpp) cc_final: 0.7973 (ttp) REVERT: c 311 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7545 (t0) REVERT: c 420 MET cc_start: 0.7564 (mmt) cc_final: 0.6610 (tpt) REVERT: b 306 ASP cc_start: 0.7738 (p0) cc_final: 0.7348 (p0) REVERT: b 418 GLU cc_start: 0.8674 (mm-30) cc_final: 0.7997 (mt-10) REVERT: b 420 MET cc_start: 0.7952 (mmt) cc_final: 0.7347 (tpt) REVERT: a 306 ASP cc_start: 0.7688 (p0) cc_final: 0.7412 (p0) REVERT: a 311 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7610 (t0) REVERT: a 332 MET cc_start: 0.6959 (tpp) cc_final: 0.6567 (tpp) REVERT: a 348 GLN cc_start: 0.5771 (mt0) cc_final: 0.5070 (tt0) REVERT: a 410 MET cc_start: 0.8607 (mtp) cc_final: 0.8019 (ttm) REVERT: a 420 MET cc_start: 0.8084 (mmt) cc_final: 0.7565 (tpt) REVERT: H 21 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7783 (mm) REVERT: H 98 ASP cc_start: 0.8155 (m-30) cc_final: 0.7930 (m-30) REVERT: H 112 TYR cc_start: 0.8280 (p90) cc_final: 0.7810 (p90) REVERT: L 18 ARG cc_start: 0.8386 (ttm170) cc_final: 0.7615 (ttp80) REVERT: L 94 LEU cc_start: 0.7884 (tp) cc_final: 0.7532 (tt) REVERT: L 99 PHE cc_start: 0.7120 (m-80) cc_final: 0.6776 (m-80) REVERT: J 30 PHE cc_start: 0.8449 (t80) cc_final: 0.8240 (t80) REVERT: J 52 TRP cc_start: 0.8400 (t60) cc_final: 0.7932 (t60) REVERT: J 98 ASP cc_start: 0.7677 (m-30) cc_final: 0.7448 (m-30) REVERT: K 17 GLU cc_start: 0.8509 (mp0) cc_final: 0.7884 (mp0) REVERT: K 42 TYR cc_start: 0.8949 (m-80) cc_final: 0.8546 (m-80) REVERT: K 99 PHE cc_start: 0.7271 (m-80) cc_final: 0.6805 (m-80) REVERT: h 5 GLN cc_start: 0.6980 (tp40) cc_final: 0.6639 (tp-100) outliers start: 55 outliers final: 35 residues processed: 293 average time/residue: 0.2802 time to fit residues: 120.4726 Evaluate side-chains 266 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 326 LEU 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 284 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 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 39 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 chunk 164 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** b 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15516 Z= 0.210 Angle : 0.692 10.674 21039 Z= 0.339 Chirality : 0.043 0.260 2604 Planarity : 0.004 0.046 2514 Dihedral : 6.917 59.727 3903 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.51 % Allowed : 14.17 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.34 (0.21), residues: 1731 helix: 1.16 (0.29), residues: 375 sheet: 0.16 (0.25), residues: 423 loop : -1.00 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 52 HIS 0.006 0.001 HIS c 305 PHE 0.022 0.001 PHE J 87 TYR 0.032 0.001 TYR b 419 ARG 0.019 0.001 ARG b 422 *********************** 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 312 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 258 time to evaluate : 1.760 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 75 MET cc_start: 0.7906 (mtm) cc_final: 0.7604 (mtm) REVERT: C 194 MET cc_start: 0.8261 (tpp) cc_final: 0.7969 (ttp) REVERT: B 67 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7412 (tt0) REVERT: c 311 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7470 (t0) REVERT: c 348 GLN cc_start: 0.5534 (mt0) cc_final: 0.5023 (tt0) REVERT: c 420 MET cc_start: 0.7706 (mmt) cc_final: 0.6755 (tpt) REVERT: A 67 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7194 (tt0) REVERT: A 151 GLU cc_start: 0.7970 (pm20) cc_final: 0.7559 (mp0) REVERT: b 332 MET cc_start: 0.7196 (tpp) cc_final: 0.6845 (tpp) REVERT: b 419 TYR cc_start: 0.7480 (t80) cc_final: 0.7234 (t80) REVERT: b 420 MET cc_start: 0.8079 (mmt) cc_final: 0.7465 (tpt) REVERT: a 311 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7437 (t70) REVERT: a 332 MET cc_start: 0.7030 (tpp) cc_final: 0.6708 (tpp) REVERT: a 348 GLN cc_start: 0.5676 (mt0) cc_final: 0.5000 (tt0) REVERT: a 410 MET cc_start: 0.8580 (mtp) cc_final: 0.8014 (ttm) REVERT: a 419 TYR cc_start: 0.6186 (OUTLIER) cc_final: 0.5582 (t80) REVERT: a 420 MET cc_start: 0.8051 (mmt) cc_final: 0.7413 (tpt) REVERT: H 98 ASP cc_start: 0.8032 (m-30) cc_final: 0.7767 (m-30) REVERT: H 108 TYR cc_start: 0.7654 (t80) cc_final: 0.7414 (t80) REVERT: H 112 TYR cc_start: 0.8210 (p90) cc_final: 0.7770 (p90) REVERT: L 18 ARG cc_start: 0.8396 (ttm170) cc_final: 0.7624 (ttp80) REVERT: L 94 LEU cc_start: 0.7846 (tp) cc_final: 0.7536 (tt) REVERT: L 99 PHE cc_start: 0.7260 (m-80) cc_final: 0.6931 (m-80) REVERT: J 52 TRP cc_start: 0.8413 (t60) cc_final: 0.7960 (t60) REVERT: J 98 ASP cc_start: 0.7572 (m-30) cc_final: 0.7310 (m-30) REVERT: K 17 GLU cc_start: 0.8508 (mp0) cc_final: 0.8004 (mp0) REVERT: K 42 TYR cc_start: 0.8825 (m-80) cc_final: 0.8513 (m-80) outliers start: 54 outliers final: 37 residues processed: 292 average time/residue: 0.2825 time to fit residues: 121.9987 Evaluate side-chains 267 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 326 LEU 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 284 MET Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain a residue 419 TYR Chi-restraints excluded: chain 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 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 5 THR Chi-restraints excluded: chain l residue 39 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 129 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15516 Z= 0.206 Angle : 0.693 10.480 21039 Z= 0.339 Chirality : 0.043 0.253 2604 Planarity : 0.004 0.064 2514 Dihedral : 6.679 57.119 3903 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.12 % Allowed : 15.46 % Favored : 81.42 % 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: -0.30 (0.21), residues: 1731 helix: 1.28 (0.29), residues: 375 sheet: 0.16 (0.25), residues: 423 loop : -1.00 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 52 HIS 0.004 0.001 HIS B 230 PHE 0.023 0.002 PHE l 99 TYR 0.037 0.001 TYR b 419 ARG 0.011 0.001 ARG l 67 *********************** 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 293 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 1.724 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 75 MET cc_start: 0.7915 (mtm) cc_final: 0.7620 (mtm) REVERT: C 153 MET cc_start: 0.8379 (ttm) cc_final: 0.8155 (ttm) REVERT: C 194 MET cc_start: 0.8240 (tpp) cc_final: 0.7923 (ttp) REVERT: c 311 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7426 (t0) REVERT: c 348 GLN cc_start: 0.5680 (mt0) cc_final: 0.5102 (tt0) REVERT: c 420 MET cc_start: 0.7731 (mmt) cc_final: 0.6850 (tpt) REVERT: A 67 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7248 (tt0) REVERT: b 332 MET cc_start: 0.7035 (tpp) cc_final: 0.6747 (tpp) REVERT: b 419 TYR cc_start: 0.7533 (t80) cc_final: 0.7272 (t80) REVERT: b 420 MET cc_start: 0.8133 (mmt) cc_final: 0.7519 (tpt) REVERT: a 303 GLU cc_start: 0.6388 (tp30) cc_final: 0.6135 (tp30) REVERT: a 311 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7479 (t0) REVERT: a 348 GLN cc_start: 0.5652 (mt0) cc_final: 0.4978 (tt0) REVERT: a 410 MET cc_start: 0.8602 (mtp) cc_final: 0.7965 (ttm) REVERT: a 419 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5508 (t80) REVERT: a 420 MET cc_start: 0.8023 (mmt) cc_final: 0.7381 (tpt) REVERT: H 98 ASP cc_start: 0.7968 (m-30) cc_final: 0.7713 (m-30) REVERT: H 108 TYR cc_start: 0.7628 (t80) cc_final: 0.7423 (t80) REVERT: L 18 ARG cc_start: 0.8389 (ttm170) cc_final: 0.7557 (ttp80) REVERT: L 94 LEU cc_start: 0.7819 (tp) cc_final: 0.7519 (tt) REVERT: L 99 PHE cc_start: 0.7216 (m-80) cc_final: 0.6859 (m-80) REVERT: J 52 TRP cc_start: 0.8306 (t60) cc_final: 0.7722 (t60) REVERT: J 98 ASP cc_start: 0.7609 (m-30) cc_final: 0.7350 (m-30) REVERT: K 17 GLU cc_start: 0.8446 (mp0) cc_final: 0.7933 (mp0) REVERT: K 42 TYR cc_start: 0.8764 (m-80) cc_final: 0.8463 (m-80) outliers start: 48 outliers final: 37 residues processed: 273 average time/residue: 0.2829 time to fit residues: 114.7183 Evaluate side-chains 263 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 326 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 345 ILE 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 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 5 THR 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 149 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15516 Z= 0.234 Angle : 0.719 12.513 21039 Z= 0.348 Chirality : 0.043 0.249 2604 Planarity : 0.004 0.055 2514 Dihedral : 6.558 48.767 3903 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.12 % Allowed : 15.92 % Favored : 80.96 % 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: -0.31 (0.21), residues: 1731 helix: 1.30 (0.29), residues: 375 sheet: 0.16 (0.25), residues: 423 loop : -1.01 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J 118 HIS 0.007 0.001 HIS l 44 PHE 0.031 0.002 PHE l 99 TYR 0.038 0.001 TYR b 419 ARG 0.011 0.001 ARG L 67 *********************** 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 286 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.7933 (mtm) cc_final: 0.7649 (mtm) REVERT: C 194 MET cc_start: 0.8294 (tpp) cc_final: 0.7963 (ttp) REVERT: B 67 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7145 (tt0) REVERT: c 348 GLN cc_start: 0.5585 (mt0) cc_final: 0.4957 (tt0) REVERT: c 420 MET cc_start: 0.7703 (mmt) cc_final: 0.6844 (tpt) REVERT: A 67 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7450 (tt0) REVERT: A 151 GLU cc_start: 0.7846 (pm20) cc_final: 0.7586 (pt0) REVERT: A 194 MET cc_start: 0.8187 (tpp) cc_final: 0.7806 (ttm) REVERT: b 332 MET cc_start: 0.7025 (tpp) cc_final: 0.6737 (tpp) REVERT: b 419 TYR cc_start: 0.7546 (t80) cc_final: 0.7297 (t80) REVERT: b 420 MET cc_start: 0.8143 (mmt) cc_final: 0.7541 (tpt) REVERT: a 311 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7521 (t0) REVERT: a 332 MET cc_start: 0.6772 (tpp) cc_final: 0.6412 (tpp) REVERT: a 348 GLN cc_start: 0.5687 (mt0) cc_final: 0.5018 (tt0) REVERT: a 410 MET cc_start: 0.8602 (mtp) cc_final: 0.7950 (ttm) REVERT: a 419 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5537 (t80) REVERT: a 420 MET cc_start: 0.8095 (mmt) cc_final: 0.7467 (tpt) REVERT: H 98 ASP cc_start: 0.8018 (m-30) cc_final: 0.7796 (m-30) REVERT: L 18 ARG cc_start: 0.8406 (ttm170) cc_final: 0.7541 (ttp80) REVERT: L 94 LEU cc_start: 0.7827 (tp) cc_final: 0.7512 (tt) REVERT: L 99 PHE cc_start: 0.7277 (m-80) cc_final: 0.6940 (m-80) REVERT: J 52 TRP cc_start: 0.8309 (t60) cc_final: 0.7788 (t60) REVERT: J 98 ASP cc_start: 0.7684 (m-30) cc_final: 0.7430 (m-30) REVERT: K 17 GLU cc_start: 0.8486 (mp0) cc_final: 0.7986 (mp0) REVERT: K 42 TYR cc_start: 0.8772 (m-80) cc_final: 0.8412 (m-80) outliers start: 48 outliers final: 39 residues processed: 266 average time/residue: 0.2807 time to fit residues: 111.5935 Evaluate side-chains 266 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 326 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 345 ILE 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 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 l residue 5 THR Chi-restraints excluded: chain l residue 39 LEU Chi-restraints excluded: chain l residue 44 HIS 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 162 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 170 optimal weight: 0.0870 chunk 156 optimal weight: 0.5980 chunk 135 optimal weight: 0.1980 chunk 14 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 324 GLN ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 HIS l 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 15516 Z= 0.200 Angle : 0.705 13.266 21039 Z= 0.341 Chirality : 0.043 0.249 2604 Planarity : 0.004 0.052 2514 Dihedral : 6.368 40.456 3903 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.92 % Allowed : 16.11 % Favored : 80.96 % 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: 1.39 (0.29), residues: 375 sheet: 0.19 (0.25), residues: 423 loop : -0.98 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP h 118 HIS 0.010 0.001 HIS l 44 PHE 0.034 0.002 PHE l 99 TYR 0.038 0.001 TYR b 419 ARG 0.011 0.001 ARG L 67 ********************** 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 286 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.7822 (mtm) cc_final: 0.7545 (mtm) REVERT: C 194 MET cc_start: 0.8291 (tpp) cc_final: 0.8017 (ttp) REVERT: B 67 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7109 (tt0) REVERT: c 303 GLU cc_start: 0.6792 (tp30) cc_final: 0.6536 (tp30) REVERT: c 324 GLN cc_start: 0.8625 (tt0) cc_final: 0.8398 (tt0) REVERT: c 348 GLN cc_start: 0.5525 (mt0) cc_final: 0.4951 (tt0) REVERT: c 420 MET cc_start: 0.7795 (mmt) cc_final: 0.6980 (tpt) REVERT: A 67 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7237 (tt0) REVERT: A 151 GLU cc_start: 0.7820 (pm20) cc_final: 0.7608 (mp0) REVERT: A 194 MET cc_start: 0.8176 (tpp) cc_final: 0.7826 (ttm) REVERT: b 419 TYR cc_start: 0.7564 (t80) cc_final: 0.7313 (t80) REVERT: b 420 MET cc_start: 0.8141 (mmt) cc_final: 0.7525 (tpt) REVERT: a 311 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7554 (t0) REVERT: a 332 MET cc_start: 0.6769 (tpp) cc_final: 0.6412 (tpp) REVERT: a 348 GLN cc_start: 0.5551 (mt0) cc_final: 0.4888 (tt0) REVERT: a 410 MET cc_start: 0.8597 (mtp) cc_final: 0.7951 (ttm) REVERT: a 419 TYR cc_start: 0.6145 (OUTLIER) cc_final: 0.5486 (t80) REVERT: a 420 MET cc_start: 0.8133 (mmt) cc_final: 0.7525 (tpt) REVERT: H 98 ASP cc_start: 0.7974 (m-30) cc_final: 0.7754 (m-30) REVERT: L 18 ARG cc_start: 0.8383 (ttm170) cc_final: 0.7510 (ttp80) REVERT: L 94 LEU cc_start: 0.7757 (tp) cc_final: 0.7465 (tt) REVERT: L 99 PHE cc_start: 0.7206 (m-80) cc_final: 0.6854 (m-80) REVERT: J 52 TRP cc_start: 0.8290 (t60) cc_final: 0.7789 (t60) REVERT: J 98 ASP cc_start: 0.7662 (m-30) cc_final: 0.7418 (m-30) REVERT: K 17 GLU cc_start: 0.8428 (mp0) cc_final: 0.7962 (mp0) REVERT: K 42 TYR cc_start: 0.8711 (m-80) cc_final: 0.8377 (m-80) REVERT: K 99 PHE cc_start: 0.7178 (m-80) cc_final: 0.6867 (m-80) outliers start: 45 outliers final: 37 residues processed: 270 average time/residue: 0.2768 time to fit residues: 111.3566 Evaluate side-chains 270 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 326 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 345 ILE 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 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 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 5 THR 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 144 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 305 HIS b 305 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.104480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081479 restraints weight = 37351.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084835 restraints weight = 19307.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087078 restraints weight = 13227.607| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15516 Z= 0.231 Angle : 0.712 12.656 21039 Z= 0.345 Chirality : 0.043 0.243 2604 Planarity : 0.004 0.051 2514 Dihedral : 6.287 38.374 3903 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.79 % Allowed : 16.37 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1731 helix: 1.39 (0.29), residues: 375 sheet: 0.14 (0.26), residues: 423 loop : -1.01 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP h 118 HIS 0.004 0.001 HIS l 44 PHE 0.031 0.002 PHE l 99 TYR 0.038 0.001 TYR b 419 ARG 0.011 0.001 ARG L 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3255.18 seconds wall clock time: 60 minutes 46.12 seconds (3646.12 seconds total)