Starting phenix.real_space_refine on Wed Feb 14 11:05:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgd_25107/02_2024/7sgd_25107.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgd_25107/02_2024/7sgd_25107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgd_25107/02_2024/7sgd_25107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgd_25107/02_2024/7sgd_25107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgd_25107/02_2024/7sgd_25107.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgd_25107/02_2024/7sgd_25107.pdb" } resolution = 3.97 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 5679 2.51 5 N 1428 2.21 5 O 1920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9120 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1371 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 3 Chain: "a" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "B" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1371 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 3 Chain: "b" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "C" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1371 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 3 Chain: "c" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "K" 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: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "N" 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: "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: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" 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: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" 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: "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: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 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: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 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: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 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: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 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: 5.12, per 1000 atoms: 0.56 Number of scatterers: 9120 At special positions: 0 Unit cell: (99.91, 93.73, 101.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 1920 8.00 N 1428 7.00 C 5679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.02 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.02 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.04 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA S 3 " - " MAN S 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " 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 Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG g 1 " - " FUC g 3 " NAG-ASN " NAG A 701 " - " ASN A 167 " " NAG B 701 " - " ASN B 167 " " NAG C 701 " - " ASN C 167 " " NAG D 1 " - " ASN A 99 " " NAG E 1 " - " ASN A 224 " " NAG F 1 " - " ASN A 79 " " NAG G 1 " - " ASN A 89 " " NAG H 1 " - " ASN A 109 " " NAG I 1 " - " ASN A 119 " " NAG J 1 " - " ASN a 365 " " NAG K 1 " - " ASN a 373 " " NAG L 1 " - " ASN a 395 " " NAG M 1 " - " ASN B 99 " " NAG N 1 " - " ASN B 224 " " NAG O 1 " - " ASN B 79 " " NAG P 1 " - " ASN B 89 " " NAG Q 1 " - " ASN B 109 " " NAG R 1 " - " ASN B 119 " " NAG S 1 " - " ASN b 365 " " NAG T 1 " - " ASN b 373 " " NAG U 1 " - " ASN b 395 " " NAG V 1 " - " ASN C 99 " " NAG W 1 " - " ASN C 224 " " NAG X 1 " - " ASN C 79 " " NAG Y 1 " - " ASN C 89 " " NAG Z 1 " - " ASN C 109 " " NAG a 701 " - " ASN a 390 " " NAG b 701 " - " ASN b 390 " " NAG c 701 " - " ASN c 390 " " NAG d 1 " - " ASN C 119 " " NAG e 1 " - " ASN c 365 " " NAG f 1 " - " ASN c 373 " " NAG g 1 " - " ASN c 395 " Time building additional restraints: 4.87 Conformation dependent library (CDL) restraints added in 1.6 seconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 42.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.951A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 130 through 144 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'a' and resid 269 through 274 removed outlier: 3.822A pdb=" N ASP a 273 " --> pdb=" O SER a 269 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR a 274 " --> pdb=" O GLU a 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 269 through 274' Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 333 through 345 removed outlier: 4.878A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.529A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 423 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.950A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 130 through 144 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'b' and resid 269 through 274 removed outlier: 3.822A pdb=" N ASP b 273 " --> pdb=" O SER b 269 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR b 274 " --> pdb=" O GLU b 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 269 through 274' Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 333 through 345 removed outlier: 4.878A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.529A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 423 Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.951A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'c' and resid 269 through 274 removed outlier: 3.822A pdb=" N ASP c 273 " --> pdb=" O SER c 269 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR c 274 " --> pdb=" O GLU c 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 269 through 274' Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 333 through 345 removed outlier: 4.878A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.530A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 423 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.667A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 102 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AA4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.666A pdb=" N HIS B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B 102 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AA8, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB1, first strand: chain 'C' and resid 84 through 89 removed outlier: 6.666A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C 102 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'c' and resid 388 through 389 384 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2406 1.33 - 1.47: 2804 1.47 - 1.61: 3934 1.61 - 1.75: 16 1.75 - 1.88: 134 Bond restraints: 9294 Sorted by residual: bond pdb=" CG TYR C 150 " pdb=" CD2 TYR C 150 " ideal model delta sigma weight residual 1.389 1.489 -0.100 2.10e-02 2.27e+03 2.27e+01 bond pdb=" CG TYR A 150 " pdb=" CD2 TYR A 150 " ideal model delta sigma weight residual 1.389 1.489 -0.100 2.10e-02 2.27e+03 2.25e+01 bond pdb=" CG TYR B 150 " pdb=" CD2 TYR B 150 " ideal model delta sigma weight residual 1.389 1.488 -0.099 2.10e-02 2.27e+03 2.24e+01 bond pdb=" CB ASN B 178 " pdb=" CG ASN B 178 " ideal model delta sigma weight residual 1.516 1.631 -0.115 2.50e-02 1.60e+03 2.12e+01 bond pdb=" CB ASN C 178 " pdb=" CG ASN C 178 " ideal model delta sigma weight residual 1.516 1.631 -0.115 2.50e-02 1.60e+03 2.12e+01 ... (remaining 9289 not shown) Histogram of bond angle deviations from ideal: 95.73 - 103.48: 105 103.48 - 111.23: 4022 111.23 - 118.98: 3961 118.98 - 126.72: 4321 126.72 - 134.47: 158 Bond angle restraints: 12567 Sorted by residual: angle pdb=" N ASN A 224 " pdb=" CA ASN A 224 " pdb=" CB ASN A 224 " ideal model delta sigma weight residual 110.26 120.80 -10.54 1.43e+00 4.89e-01 5.43e+01 angle pdb=" N ASN C 224 " pdb=" CA ASN C 224 " pdb=" CB ASN C 224 " ideal model delta sigma weight residual 110.26 120.78 -10.52 1.43e+00 4.89e-01 5.41e+01 angle pdb=" N ASN B 224 " pdb=" CA ASN B 224 " pdb=" CB ASN B 224 " ideal model delta sigma weight residual 110.26 120.77 -10.51 1.43e+00 4.89e-01 5.40e+01 angle pdb=" N VAL C 65 " pdb=" CA VAL C 65 " pdb=" C VAL C 65 " ideal model delta sigma weight residual 113.43 121.13 -7.70 1.09e+00 8.42e-01 5.00e+01 angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 113.43 121.11 -7.68 1.09e+00 8.42e-01 4.96e+01 ... (remaining 12562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 6222 21.39 - 42.78: 174 42.78 - 64.17: 54 64.17 - 85.56: 42 85.56 - 106.95: 24 Dihedral angle restraints: 6516 sinusoidal: 3558 harmonic: 2958 Sorted by residual: dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 231 " pdb=" CB CYS B 231 " ideal model delta sinusoidal sigma weight residual 93.00 155.46 -62.46 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual 93.00 155.45 -62.45 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual 93.00 155.45 -62.45 1 1.00e+01 1.00e-02 5.16e+01 ... (remaining 6513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 1474 0.294 - 0.589: 119 0.589 - 0.883: 3 0.883 - 1.177: 0 1.177 - 1.472: 3 Chirality restraints: 1599 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 ... (remaining 1596 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.173 2.00e-02 2.50e+03 1.43e-01 2.56e+02 pdb=" C7 NAG N 2 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.233 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.173 2.00e-02 2.50e+03 1.43e-01 2.56e+02 pdb=" C7 NAG E 2 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.233 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " 0.173 2.00e-02 2.50e+03 1.43e-01 2.56e+02 pdb=" C7 NAG W 2 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " -0.233 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " -0.019 2.00e-02 2.50e+03 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 4657 2.96 - 3.45: 8715 3.45 - 3.93: 15253 3.93 - 4.42: 17664 4.42 - 4.90: 26323 Nonbonded interactions: 72612 Sorted by model distance: nonbonded pdb=" NZ LYS a 304 " pdb=" OE2 GLU c 303 " model vdw 2.477 2.520 nonbonded pdb=" OE2 GLU b 303 " pdb=" NZ LYS c 304 " model vdw 2.477 2.520 nonbonded pdb=" OE2 GLU a 303 " pdb=" NZ LYS b 304 " model vdw 2.477 2.520 nonbonded pdb=" OG SER b 367 " pdb=" N LYS b 368 " model vdw 2.486 2.520 nonbonded pdb=" OG SER c 367 " pdb=" N LYS c 368 " model vdw 2.487 2.520 ... (remaining 72607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'e' } 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.750 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.020 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.024 0.115 9294 Z= 1.497 Angle : 1.797 10.537 12567 Z= 1.150 Chirality : 0.166 1.472 1599 Planarity : 0.012 0.143 1482 Dihedral : 14.410 106.948 4545 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.24), residues: 984 helix: 0.43 (0.24), residues: 354 sheet: 0.82 (0.44), residues: 141 loop : -0.19 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.006 TRP a 283 HIS 0.006 0.002 HIS B 124 PHE 0.016 0.005 PHE a 399 TYR 0.051 0.009 TYR b 363 ARG 0.004 0.001 ARG a 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8548 (t0) cc_final: 0.8036 (t0) REVERT: A 220 LEU cc_start: 0.9228 (tp) cc_final: 0.8993 (tt) REVERT: a 311 ASP cc_start: 0.9105 (m-30) cc_final: 0.8876 (m-30) REVERT: a 313 LEU cc_start: 0.9765 (tp) cc_final: 0.9549 (tp) REVERT: a 357 ASP cc_start: 0.9090 (t70) cc_final: 0.8867 (t0) REVERT: a 408 ASP cc_start: 0.8719 (m-30) cc_final: 0.8202 (m-30) REVERT: a 409 ASN cc_start: 0.9153 (m-40) cc_final: 0.8832 (t0) REVERT: a 416 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8889 (mt0) REVERT: a 417 LYS cc_start: 0.9380 (mttt) cc_final: 0.9012 (ttpp) REVERT: B 78 LEU cc_start: 0.9633 (mt) cc_final: 0.9381 (mp) REVERT: B 130 ASP cc_start: 0.8481 (t0) cc_final: 0.8032 (t0) REVERT: B 220 LEU cc_start: 0.9271 (tp) cc_final: 0.9007 (tt) REVERT: b 267 SER cc_start: 0.8975 (p) cc_final: 0.8588 (t) REVERT: b 311 ASP cc_start: 0.9045 (m-30) cc_final: 0.8821 (m-30) REVERT: b 313 LEU cc_start: 0.9758 (tp) cc_final: 0.9489 (tp) REVERT: b 346 ASN cc_start: 0.9314 (t0) cc_final: 0.9064 (t0) REVERT: b 357 ASP cc_start: 0.9077 (t70) cc_final: 0.8848 (t0) REVERT: b 408 ASP cc_start: 0.8772 (m-30) cc_final: 0.8414 (m-30) REVERT: b 409 ASN cc_start: 0.9123 (m-40) cc_final: 0.8143 (m-40) REVERT: b 411 ILE cc_start: 0.9472 (mt) cc_final: 0.9253 (mm) REVERT: b 416 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8979 (mm-40) REVERT: b 417 LYS cc_start: 0.9354 (mttt) cc_final: 0.9041 (ttpp) REVERT: C 78 LEU cc_start: 0.9615 (mt) cc_final: 0.9392 (mp) REVERT: C 130 ASP cc_start: 0.8407 (t0) cc_final: 0.7960 (t0) REVERT: C 191 PHE cc_start: 0.9267 (t80) cc_final: 0.9057 (t80) REVERT: C 220 LEU cc_start: 0.9267 (tp) cc_final: 0.9030 (tt) REVERT: c 313 LEU cc_start: 0.9775 (tp) cc_final: 0.9493 (tp) REVERT: c 346 ASN cc_start: 0.9278 (t0) cc_final: 0.8887 (t0) REVERT: c 347 ASP cc_start: 0.8914 (p0) cc_final: 0.8519 (p0) REVERT: c 409 ASN cc_start: 0.9162 (m-40) cc_final: 0.8244 (m-40) REVERT: c 416 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8838 (tp-100) REVERT: c 417 LYS cc_start: 0.9356 (mttt) cc_final: 0.8994 (ttpp) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.2375 time to fit residues: 146.1539 Evaluate side-chains 284 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 230 HIS ** a 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS B 232 GLN ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 GLN ** b 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS ** c 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9294 Z= 0.305 Angle : 0.914 13.292 12567 Z= 0.472 Chirality : 0.051 0.350 1599 Planarity : 0.005 0.057 1482 Dihedral : 13.538 84.070 2613 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.48 % Allowed : 17.65 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.62 (0.25), residues: 984 helix: 1.44 (0.27), residues: 366 sheet: 1.61 (0.43), residues: 132 loop : -0.74 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 227 HIS 0.010 0.002 HIS C 93 PHE 0.026 0.003 PHE A 191 TYR 0.024 0.002 TYR C 166 ARG 0.007 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 293 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8415 (t0) cc_final: 0.8019 (t0) REVERT: a 300 LYS cc_start: 0.9371 (mmtm) cc_final: 0.8863 (mptt) REVERT: a 307 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8275 (mm-30) REVERT: a 313 LEU cc_start: 0.9746 (tp) cc_final: 0.9406 (tp) REVERT: a 357 ASP cc_start: 0.9011 (t70) cc_final: 0.8731 (t0) REVERT: B 130 ASP cc_start: 0.8238 (t0) cc_final: 0.7804 (t0) REVERT: B 211 ASP cc_start: 0.8058 (p0) cc_final: 0.7837 (p0) REVERT: b 261 THR cc_start: 0.7892 (p) cc_final: 0.7674 (p) REVERT: b 313 LEU cc_start: 0.9762 (tp) cc_final: 0.9437 (tp) REVERT: b 357 ASP cc_start: 0.8953 (t70) cc_final: 0.8693 (t0) REVERT: C 100 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7170 (mm-30) REVERT: C 130 ASP cc_start: 0.8194 (t0) cc_final: 0.7876 (t0) REVERT: c 261 THR cc_start: 0.8044 (p) cc_final: 0.7824 (p) REVERT: c 278 TYR cc_start: 0.8072 (t80) cc_final: 0.7808 (t80) REVERT: c 306 ASP cc_start: 0.8197 (t0) cc_final: 0.7820 (t70) REVERT: c 307 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7865 (mm-30) REVERT: c 308 GLU cc_start: 0.8883 (mp0) cc_final: 0.8620 (pm20) REVERT: c 311 ASP cc_start: 0.8879 (m-30) cc_final: 0.8512 (t0) REVERT: c 313 LEU cc_start: 0.9718 (tp) cc_final: 0.9383 (tp) REVERT: c 403 ILE cc_start: 0.9645 (mt) cc_final: 0.9394 (tt) outliers start: 50 outliers final: 26 residues processed: 319 average time/residue: 0.2054 time to fit residues: 90.2718 Evaluate side-chains 279 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 253 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain a residue 269 SER Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain b residue 269 SER Chi-restraints excluded: chain b residue 305 HIS Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 421 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 90 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN B 185 ASN C 69 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 185 ASN C 232 GLN c 416 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9294 Z= 0.220 Angle : 0.807 10.530 12567 Z= 0.404 Chirality : 0.048 0.270 1599 Planarity : 0.004 0.045 1482 Dihedral : 11.511 71.131 2613 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.48 % Allowed : 20.83 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 984 helix: 1.25 (0.27), residues: 366 sheet: 1.03 (0.48), residues: 117 loop : -0.76 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 227 HIS 0.004 0.001 HIS b 354 PHE 0.022 0.002 PHE B 157 TYR 0.022 0.002 TYR C 241 ARG 0.003 0.000 ARG b 422 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 272 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8288 (t0) cc_final: 0.7828 (t70) REVERT: A 140 PHE cc_start: 0.9174 (t80) cc_final: 0.8918 (t80) REVERT: A 211 ASP cc_start: 0.8423 (p0) cc_final: 0.7983 (p0) REVERT: a 261 THR cc_start: 0.8058 (p) cc_final: 0.7848 (p) REVERT: a 300 LYS cc_start: 0.9395 (mmtm) cc_final: 0.8870 (mptt) REVERT: a 306 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: a 351 MET cc_start: 0.8843 (mmp) cc_final: 0.8552 (mmp) REVERT: a 357 ASP cc_start: 0.8967 (t70) cc_final: 0.8703 (t0) REVERT: a 413 GLU cc_start: 0.8725 (pp20) cc_final: 0.8131 (tm-30) REVERT: B 130 ASP cc_start: 0.8181 (t0) cc_final: 0.7931 (t0) REVERT: b 261 THR cc_start: 0.7967 (p) cc_final: 0.7763 (p) REVERT: b 313 LEU cc_start: 0.9638 (tp) cc_final: 0.9305 (tp) REVERT: b 357 ASP cc_start: 0.8910 (t70) cc_final: 0.8685 (t0) REVERT: b 406 GLN cc_start: 0.9443 (tp40) cc_final: 0.9157 (tp40) REVERT: b 420 MET cc_start: 0.8646 (mmp) cc_final: 0.7665 (mmt) REVERT: C 100 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7152 (mm-30) REVERT: C 130 ASP cc_start: 0.8012 (t0) cc_final: 0.7569 (t70) REVERT: c 261 THR cc_start: 0.8059 (p) cc_final: 0.7834 (p) REVERT: c 278 TYR cc_start: 0.8057 (t80) cc_final: 0.7800 (t80) REVERT: c 300 LYS cc_start: 0.9346 (mmtm) cc_final: 0.8996 (mptt) REVERT: c 311 ASP cc_start: 0.8790 (m-30) cc_final: 0.8484 (t0) REVERT: c 313 LEU cc_start: 0.9669 (tp) cc_final: 0.9340 (tp) REVERT: c 417 LYS cc_start: 0.9298 (pttp) cc_final: 0.9024 (pttp) outliers start: 50 outliers final: 31 residues processed: 301 average time/residue: 0.2170 time to fit residues: 88.6252 Evaluate side-chains 263 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain a residue 269 SER Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 306 ASP Chi-restraints excluded: chain a residue 325 ARG Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.0980 chunk 47 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** a 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** b 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9294 Z= 0.277 Angle : 0.788 7.715 12567 Z= 0.390 Chirality : 0.048 0.279 1599 Planarity : 0.004 0.045 1482 Dihedral : 10.371 63.588 2613 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.70 % Allowed : 22.26 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.25), residues: 984 helix: 1.38 (0.27), residues: 366 sheet: 0.85 (0.48), residues: 120 loop : -0.76 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 227 HIS 0.005 0.001 HIS A 179 PHE 0.019 0.002 PHE B 157 TYR 0.025 0.002 TYR A 129 ARG 0.004 0.001 ARG a 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 231 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8356 (t0) cc_final: 0.7881 (t70) REVERT: A 211 ASP cc_start: 0.8436 (p0) cc_final: 0.8003 (p0) REVERT: a 300 LYS cc_start: 0.9448 (mmtm) cc_final: 0.8947 (mptt) REVERT: a 306 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: a 357 ASP cc_start: 0.9107 (t70) cc_final: 0.8796 (t0) REVERT: a 413 GLU cc_start: 0.8543 (pp20) cc_final: 0.7829 (tm-30) REVERT: a 417 LYS cc_start: 0.9347 (pttp) cc_final: 0.8745 (pttm) REVERT: B 130 ASP cc_start: 0.8162 (t0) cc_final: 0.7931 (t0) REVERT: b 261 THR cc_start: 0.8177 (p) cc_final: 0.7969 (p) REVERT: b 313 LEU cc_start: 0.9636 (tp) cc_final: 0.9278 (tp) REVERT: b 357 ASP cc_start: 0.9054 (t70) cc_final: 0.8751 (t0) REVERT: C 100 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7285 (mm-30) REVERT: C 130 ASP cc_start: 0.8055 (t0) cc_final: 0.7631 (t70) REVERT: c 278 TYR cc_start: 0.8158 (t80) cc_final: 0.7954 (t80) REVERT: c 300 LYS cc_start: 0.9412 (mmtm) cc_final: 0.9097 (mptt) REVERT: c 311 ASP cc_start: 0.8857 (m-30) cc_final: 0.8497 (t0) REVERT: c 313 LEU cc_start: 0.9686 (tp) cc_final: 0.9367 (tp) REVERT: c 417 LYS cc_start: 0.9326 (pttp) cc_final: 0.8941 (pttp) outliers start: 52 outliers final: 38 residues processed: 266 average time/residue: 0.2167 time to fit residues: 78.5713 Evaluate side-chains 242 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 269 SER Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 306 ASP Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 350 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** a 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 416 GLN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9294 Z= 0.282 Angle : 0.775 6.798 12567 Z= 0.385 Chirality : 0.048 0.306 1599 Planarity : 0.004 0.039 1482 Dihedral : 9.652 57.036 2613 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 6.36 % Allowed : 21.27 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 984 helix: 1.35 (0.27), residues: 369 sheet: 0.81 (0.48), residues: 120 loop : -0.92 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 210 HIS 0.004 0.001 HIS A 179 PHE 0.018 0.002 PHE C 157 TYR 0.026 0.002 TYR B 241 ARG 0.003 0.001 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 210 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8432 (t0) cc_final: 0.8009 (t70) REVERT: a 300 LYS cc_start: 0.9471 (mmtm) cc_final: 0.9022 (mptt) REVERT: a 306 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: a 357 ASP cc_start: 0.9166 (t70) cc_final: 0.8826 (t0) REVERT: a 408 ASP cc_start: 0.8864 (m-30) cc_final: 0.8663 (m-30) REVERT: a 413 GLU cc_start: 0.8593 (pp20) cc_final: 0.7939 (tm-30) REVERT: a 417 LYS cc_start: 0.9359 (pttp) cc_final: 0.8814 (pttm) REVERT: B 129 TYR cc_start: 0.6820 (m-10) cc_final: 0.6619 (m-10) REVERT: B 130 ASP cc_start: 0.8125 (t0) cc_final: 0.7754 (t70) REVERT: B 194 MET cc_start: 0.9179 (tpp) cc_final: 0.8634 (tpp) REVERT: B 211 ASP cc_start: 0.8210 (p0) cc_final: 0.7447 (p0) REVERT: b 261 THR cc_start: 0.8395 (p) cc_final: 0.8194 (p) REVERT: b 313 LEU cc_start: 0.9649 (tp) cc_final: 0.9329 (tp) REVERT: b 357 ASP cc_start: 0.9123 (t70) cc_final: 0.8785 (t0) REVERT: C 130 ASP cc_start: 0.7976 (t0) cc_final: 0.7540 (t70) REVERT: C 194 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8912 (tpp) REVERT: c 300 LYS cc_start: 0.9444 (mmtm) cc_final: 0.9130 (mptt) REVERT: c 311 ASP cc_start: 0.8865 (m-30) cc_final: 0.8537 (t0) REVERT: c 313 LEU cc_start: 0.9665 (tp) cc_final: 0.9334 (tp) REVERT: c 347 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8352 (p0) outliers start: 58 outliers final: 42 residues processed: 252 average time/residue: 0.2118 time to fit residues: 73.7421 Evaluate side-chains 244 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 199 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 269 SER Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 306 ASP Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 350 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** b 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9294 Z= 0.236 Angle : 0.774 9.463 12567 Z= 0.380 Chirality : 0.048 0.296 1599 Planarity : 0.004 0.041 1482 Dihedral : 9.386 55.500 2613 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.47 % Allowed : 21.82 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 984 helix: 1.46 (0.28), residues: 369 sheet: 0.79 (0.49), residues: 120 loop : -0.95 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 227 HIS 0.007 0.001 HIS a 354 PHE 0.018 0.002 PHE C 157 TYR 0.022 0.002 TYR A 241 ARG 0.003 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 207 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8378 (t0) cc_final: 0.7923 (t70) REVERT: a 278 TYR cc_start: 0.7780 (t80) cc_final: 0.7556 (t80) REVERT: a 300 LYS cc_start: 0.9481 (mmtm) cc_final: 0.9027 (mptt) REVERT: a 306 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: a 408 ASP cc_start: 0.8829 (m-30) cc_final: 0.8537 (m-30) REVERT: a 413 GLU cc_start: 0.8570 (pp20) cc_final: 0.7872 (tm-30) REVERT: a 417 LYS cc_start: 0.9354 (pttp) cc_final: 0.8818 (pttm) REVERT: B 129 TYR cc_start: 0.6575 (m-10) cc_final: 0.6331 (m-10) REVERT: B 130 ASP cc_start: 0.8070 (t0) cc_final: 0.7730 (t70) REVERT: B 194 MET cc_start: 0.9146 (tpp) cc_final: 0.8721 (tpp) REVERT: b 313 LEU cc_start: 0.9614 (tp) cc_final: 0.9259 (tp) REVERT: b 357 ASP cc_start: 0.9113 (t70) cc_final: 0.8757 (t0) REVERT: C 129 TYR cc_start: 0.6397 (m-10) cc_final: 0.6176 (m-10) REVERT: C 130 ASP cc_start: 0.7957 (t0) cc_final: 0.7541 (t70) REVERT: C 194 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8857 (tpp) REVERT: c 300 LYS cc_start: 0.9443 (mmtm) cc_final: 0.9131 (mptt) REVERT: c 311 ASP cc_start: 0.8844 (m-30) cc_final: 0.8487 (t0) REVERT: c 313 LEU cc_start: 0.9607 (tp) cc_final: 0.9246 (tp) outliers start: 59 outliers final: 43 residues processed: 246 average time/residue: 0.2160 time to fit residues: 74.4451 Evaluate side-chains 237 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 192 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 269 SER Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 306 ASP Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 350 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** a 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN b 416 GLN C 185 ASN ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9294 Z= 0.271 Angle : 0.795 16.272 12567 Z= 0.391 Chirality : 0.049 0.364 1599 Planarity : 0.004 0.040 1482 Dihedral : 9.213 55.607 2613 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.48 % Allowed : 22.04 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.26), residues: 984 helix: 1.35 (0.27), residues: 369 sheet: 0.64 (0.49), residues: 120 loop : -1.02 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 227 HIS 0.005 0.001 HIS A 179 PHE 0.018 0.002 PHE C 157 TYR 0.027 0.002 TYR A 241 ARG 0.003 0.000 ARG a 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 192 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8433 (t0) cc_final: 0.7994 (t70) REVERT: a 300 LYS cc_start: 0.9525 (mmtm) cc_final: 0.9101 (mptt) REVERT: a 311 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8593 (t0) REVERT: a 408 ASP cc_start: 0.8851 (m-30) cc_final: 0.8438 (m-30) REVERT: a 413 GLU cc_start: 0.8605 (pp20) cc_final: 0.8252 (tm-30) REVERT: B 96 MET cc_start: 0.8683 (ttp) cc_final: 0.8415 (ttm) REVERT: B 130 ASP cc_start: 0.8128 (t0) cc_final: 0.7784 (t70) REVERT: B 194 MET cc_start: 0.9180 (tpp) cc_final: 0.8716 (tpp) REVERT: b 313 LEU cc_start: 0.9652 (tp) cc_final: 0.9333 (tp) REVERT: b 357 ASP cc_start: 0.9192 (t70) cc_final: 0.8840 (t0) REVERT: b 414 MET cc_start: 0.8711 (tpp) cc_final: 0.8470 (tpp) REVERT: C 130 ASP cc_start: 0.7963 (t0) cc_final: 0.7531 (t70) REVERT: c 300 LYS cc_start: 0.9467 (mmtm) cc_final: 0.9167 (mptt) REVERT: c 311 ASP cc_start: 0.8898 (m-30) cc_final: 0.8592 (t0) REVERT: c 325 ARG cc_start: 0.8554 (mmm160) cc_final: 0.7964 (mmm160) REVERT: c 351 MET cc_start: 0.8683 (mmp) cc_final: 0.8399 (mmp) outliers start: 50 outliers final: 36 residues processed: 229 average time/residue: 0.2075 time to fit residues: 65.1475 Evaluate side-chains 208 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 350 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN ** c 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9294 Z= 0.446 Angle : 0.905 13.580 12567 Z= 0.441 Chirality : 0.051 0.314 1599 Planarity : 0.005 0.040 1482 Dihedral : 9.390 56.609 2613 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 6.25 % Allowed : 21.93 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.26), residues: 984 helix: 1.21 (0.27), residues: 369 sheet: 0.51 (0.48), residues: 120 loop : -1.27 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 227 HIS 0.006 0.001 HIS B 93 PHE 0.020 0.003 PHE b 309 TYR 0.029 0.002 TYR B 241 ARG 0.003 0.000 ARG c 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 170 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8388 (t0) cc_final: 0.7948 (t70) REVERT: a 311 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8627 (t0) REVERT: a 405 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8489 (tm-30) REVERT: a 408 ASP cc_start: 0.8928 (m-30) cc_final: 0.8455 (m-30) REVERT: a 413 GLU cc_start: 0.8648 (pp20) cc_final: 0.8329 (tm-30) REVERT: B 130 ASP cc_start: 0.8325 (t0) cc_final: 0.7961 (t70) REVERT: b 313 LEU cc_start: 0.9685 (tp) cc_final: 0.9380 (tp) REVERT: b 357 ASP cc_start: 0.9361 (t70) cc_final: 0.8915 (t0) REVERT: C 80 MET cc_start: 0.9183 (mpp) cc_final: 0.8720 (mmt) REVERT: C 130 ASP cc_start: 0.8107 (t0) cc_final: 0.7648 (t70) REVERT: c 311 ASP cc_start: 0.8925 (m-30) cc_final: 0.8640 (t0) REVERT: c 325 ARG cc_start: 0.8600 (mmm160) cc_final: 0.8058 (mmm160) outliers start: 57 outliers final: 49 residues processed: 214 average time/residue: 0.1827 time to fit residues: 55.6860 Evaluate side-chains 214 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 164 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 269 SER Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 279 CYS Chi-restraints excluded: chain a residue 298 VAL Chi-restraints excluded: chain a residue 305 HIS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 350 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 401 ASP Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 416 GLN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9294 Z= 0.228 Angle : 0.797 12.737 12567 Z= 0.388 Chirality : 0.049 0.280 1599 Planarity : 0.004 0.041 1482 Dihedral : 8.984 55.554 2613 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.28 % Allowed : 24.23 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.26), residues: 984 helix: 1.32 (0.27), residues: 369 sheet: 0.73 (0.49), residues: 120 loop : -1.03 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 227 HIS 0.004 0.001 HIS C 92 PHE 0.018 0.002 PHE B 157 TYR 0.041 0.002 TYR C 241 ARG 0.003 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 1.090 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: A 130 ASP cc_start: 0.8495 (t0) cc_final: 0.8056 (t70) REVERT: A 218 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: a 408 ASP cc_start: 0.8853 (m-30) cc_final: 0.8377 (m-30) REVERT: a 413 GLU cc_start: 0.8602 (pp20) cc_final: 0.8310 (tm-30) REVERT: B 94 TYR cc_start: 0.8929 (t80) cc_final: 0.8444 (t80) REVERT: B 130 ASP cc_start: 0.8216 (t0) cc_final: 0.7818 (t70) REVERT: b 313 LEU cc_start: 0.9631 (tp) cc_final: 0.9287 (tp) REVERT: b 357 ASP cc_start: 0.9186 (t70) cc_final: 0.8819 (t0) REVERT: b 414 MET cc_start: 0.8667 (tpp) cc_final: 0.8366 (tpp) REVERT: C 80 MET cc_start: 0.9058 (mpp) cc_final: 0.8570 (mmt) REVERT: C 130 ASP cc_start: 0.8027 (t0) cc_final: 0.7599 (t70) REVERT: C 218 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: C 235 ARG cc_start: 0.8916 (tpp80) cc_final: 0.8171 (ttm-80) REVERT: c 311 ASP cc_start: 0.8914 (m-30) cc_final: 0.8598 (t0) REVERT: c 325 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8052 (mmm160) outliers start: 39 outliers final: 31 residues processed: 225 average time/residue: 0.2033 time to fit residues: 63.9936 Evaluate side-chains 213 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 279 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 350 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 416 GLN ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS C 185 ASN ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN ** c 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.6886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9294 Z= 0.294 Angle : 0.842 12.567 12567 Z= 0.410 Chirality : 0.049 0.281 1599 Planarity : 0.004 0.040 1482 Dihedral : 9.137 55.519 2613 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.95 % Allowed : 25.33 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.27), residues: 984 helix: 1.80 (0.28), residues: 345 sheet: 0.68 (0.49), residues: 120 loop : -0.89 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 227 HIS 0.005 0.001 HIS C 124 PHE 0.019 0.002 PHE B 157 TYR 0.044 0.002 TYR C 241 ARG 0.013 0.001 ARG a 422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8379 (t0) cc_final: 0.7969 (t70) REVERT: a 405 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8448 (tm-30) REVERT: a 408 ASP cc_start: 0.8871 (m-30) cc_final: 0.8359 (m-30) REVERT: a 413 GLU cc_start: 0.8629 (pp20) cc_final: 0.8308 (tm-30) REVERT: B 76 GLU cc_start: 0.8640 (tt0) cc_final: 0.8098 (tm-30) REVERT: B 130 ASP cc_start: 0.8269 (t0) cc_final: 0.7863 (t0) REVERT: b 313 LEU cc_start: 0.9656 (tp) cc_final: 0.9337 (tp) REVERT: b 357 ASP cc_start: 0.9249 (t70) cc_final: 0.8883 (t0) REVERT: b 414 MET cc_start: 0.8700 (tpp) cc_final: 0.8400 (tpp) REVERT: C 130 ASP cc_start: 0.8071 (t0) cc_final: 0.7619 (t70) REVERT: C 218 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8298 (pm20) REVERT: c 311 ASP cc_start: 0.8926 (m-30) cc_final: 0.8646 (t0) outliers start: 36 outliers final: 32 residues processed: 212 average time/residue: 0.1889 time to fit residues: 57.1295 Evaluate side-chains 207 residues out of total 912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 279 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 124 HIS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 350 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 401 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** a 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** b 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS c 319 ASN ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN ** c 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.054431 restraints weight = 30288.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.056673 restraints weight = 17423.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.058189 restraints weight = 12614.184| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9294 Z= 0.252 Angle : 0.843 13.204 12567 Z= 0.405 Chirality : 0.048 0.274 1599 Planarity : 0.004 0.041 1482 Dihedral : 8.984 55.294 2613 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.95 % Allowed : 25.77 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.27), residues: 984 helix: 1.74 (0.28), residues: 345 sheet: 0.79 (0.50), residues: 117 loop : -0.88 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 227 HIS 0.006 0.001 HIS C 124 PHE 0.019 0.002 PHE C 157 TYR 0.041 0.002 TYR C 241 ARG 0.010 0.001 ARG a 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.76 seconds wall clock time: 38 minutes 59.61 seconds (2339.61 seconds total)