Starting phenix.real_space_refine on Sat Sep 28 19:28:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/09_2024/8g3v_29710.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/09_2024/8g3v_29710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/09_2024/8g3v_29710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/09_2024/8g3v_29710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/09_2024/8g3v_29710.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3v_29710/09_2024/8g3v_29710.cif" } resolution = 2.2 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= 0.048 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 116 5.16 5 C 12484 2.51 5 N 3416 2.21 5 O 4024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20045 Number of models: 1 Model: "" Number of chains: 28 Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "A" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "M" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "N" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 375} Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "U" 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "X" 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 13.72, per 1000 atoms: 0.68 Number of scatterers: 20045 At special positions: 0 Unit cell: (131.97, 131.97, 102.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 116 16.00 O 4024 8.00 N 3416 7.00 C 12484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.06 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.07 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.08 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.11 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.11 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.10 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.10 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.15 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.06 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.07 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.11 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.11 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.10 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.10 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.15 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.05 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.07 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 417 " distance=2.06 Simple disulfide: pdb=" SG CYS I 124 " - pdb=" SG CYS I 129 " distance=2.07 Simple disulfide: pdb=" SG CYS I 175 " - pdb=" SG CYS I 193 " distance=2.03 Simple disulfide: pdb=" SG CYS I 183 " - pdb=" SG CYS I 230 " distance=2.08 Simple disulfide: pdb=" SG CYS I 232 " - pdb=" SG CYS I 237 " distance=2.11 Simple disulfide: pdb=" SG CYS I 278 " - pdb=" SG CYS I 291 " distance=2.11 Simple disulfide: pdb=" SG CYS I 280 " - pdb=" SG CYS I 289 " distance=2.10 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.10 Simple disulfide: pdb=" SG CYS I 421 " - pdb=" SG CYS I 447 " distance=2.15 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.07 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.06 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.07 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.08 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.11 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.11 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.10 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.10 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.15 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN Q 4 " - " MAN Q 5 " " MAN T 4 " - " MAN T 5 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " MAN F 6 " - " MAN F 7 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 6 " - " MAN Q 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA W 3 " - " MAN W 4 " " MAN W 6 " - " MAN W 7 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " MAN F 6 " - " MAN F 8 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 6 " - " MAN Q 8 " " BMA T 3 " - " MAN T 6 " " MAN T 6 " - " MAN T 8 " " BMA W 3 " - " MAN W 6 " " MAN W 6 " - " MAN W 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG K 1 " - " NAG K 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN G 86 " " NAG F 1 " - " ASN G 200 " " NAG G1101 " - " ASN G 146 " " NAG G1102 " - " ASN G 367 " " NAG H1101 " - " ASN H 146 " " NAG H1102 " - " ASN H 367 " " NAG I1101 " - " ASN I 146 " " NAG I1102 " - " ASN I 367 " " NAG J1101 " - " ASN J 146 " " NAG J1102 " - " ASN J 367 " " NAG K 1 " - " ASN G 234 " " NAG P 1 " - " ASN H 86 " " NAG Q 1 " - " ASN H 200 " " NAG R 1 " - " ASN H 234 " " NAG S 1 " - " ASN I 86 " " NAG T 1 " - " ASN I 200 " " NAG U 1 " - " ASN I 234 " " NAG V 1 " - " ASN J 86 " " NAG W 1 " - " ASN J 200 " " NAG X 1 " - " ASN J 234 " Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 2.7 seconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.1% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.690A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.560A pdb=" N LYS A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.691A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.558A pdb=" N LYS B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.659A pdb=" N PHE M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.689A pdb=" N ASN I 146 " --> pdb=" O VAL I 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.561A pdb=" N LYS C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.679A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.561A pdb=" N LYS D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.658A pdb=" N PHE O 83 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.802A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.796A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.116A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP G 213 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.527A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.381A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 353 through 356 removed outlier: 7.082A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.497A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.487A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.241A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.249A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 40 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.391A pdb=" N PHE A 117 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER L 67 " --> pdb=" O GLN L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.474A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.804A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.797A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.121A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP H 213 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.524A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.381A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 353 through 356 removed outlier: 7.085A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.418A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.500A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.525A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.252A pdb=" N LEU B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.391A pdb=" N PHE B 117 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AC5, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER M 67 " --> pdb=" O GLN M 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.475A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 96 through 102 removed outlier: 3.801A pdb=" N GLY I 96 " --> pdb=" O THR I 449 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL I 445 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS I 102 " --> pdb=" O ILE I 443 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE I 443 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG I 420 " --> pdb=" O GLY I 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 115 through 124 removed outlier: 4.795A pdb=" N TRP I 115 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR I 138 " --> pdb=" O TRP I 115 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR I 117 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN I 136 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU I 119 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU I 134 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR I 157 " --> pdb=" O GLY I 135 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU I 158 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS I 172 " --> pdb=" O MET I 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 179 through 184 removed outlier: 4.114A pdb=" N ASP I 197 " --> pdb=" O ASN I 200 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP I 213 " --> pdb=" O PHE I 205 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR I 207 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU I 211 " --> pdb=" O TYR I 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 231 through 233 removed outlier: 6.524A pdb=" N GLU I 258 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE I 262 " --> pdb=" O GLU I 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 276 through 283 removed outlier: 5.384A pdb=" N GLU I 277 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG I 292 " --> pdb=" O GLU I 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 353 through 356 removed outlier: 7.093A pdb=" N ASP I 402 " --> pdb=" O GLY I 373 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N GLU I 375 " --> pdb=" O ARG I 400 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N ARG I 400 " --> pdb=" O GLU I 375 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N PHE I 377 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 13.491A pdb=" N VAL I 398 " --> pdb=" O PHE I 377 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N VAL I 379 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL I 396 " --> pdb=" O VAL I 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.261A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.394A pdb=" N PHE C 117 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD8, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.849A pdb=" N GLN N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER N 67 " --> pdb=" O GLN N 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.476A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.801A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.798A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.119A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP J 213 " --> pdb=" O PHE J 205 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 231 through 233 removed outlier: 6.525A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.383A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 353 through 356 removed outlier: 7.092A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.493A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.245A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.259A pdb=" N LEU D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 40 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.394A pdb=" N PHE D 117 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AF2, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.850A pdb=" N GLN O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER O 67 " --> pdb=" O GLN O 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.477A pdb=" N LEU O 33 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1728 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: 7.11 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3703 1.32 - 1.45: 5439 1.45 - 1.57: 11206 1.57 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 20492 Sorted by residual: bond pdb=" N VAL O 58 " pdb=" CA VAL O 58 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.00e+01 bond pdb=" CA SER J 457 " pdb=" CB SER J 457 " ideal model delta sigma weight residual 1.534 1.460 0.074 1.72e-02 3.38e+03 1.85e+01 bond pdb=" CA SER H 457 " pdb=" CB SER H 457 " ideal model delta sigma weight residual 1.534 1.463 0.070 1.72e-02 3.38e+03 1.67e+01 bond pdb=" N VAL G 165 " pdb=" CA VAL G 165 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.61e+01 bond pdb=" N VAL I 165 " pdb=" CA VAL I 165 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.61e+01 ... (remaining 20487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 24137 2.38 - 4.77: 3467 4.77 - 7.15: 203 7.15 - 9.53: 13 9.53 - 11.91: 4 Bond angle restraints: 27824 Sorted by residual: angle pdb=" C ARG I 430 " pdb=" N LYS I 431 " pdb=" CA LYS I 431 " ideal model delta sigma weight residual 121.54 133.45 -11.91 1.91e+00 2.74e-01 3.89e+01 angle pdb=" C ARG G 430 " pdb=" N LYS G 431 " pdb=" CA LYS G 431 " ideal model delta sigma weight residual 121.54 133.42 -11.88 1.91e+00 2.74e-01 3.87e+01 angle pdb=" C ARG J 430 " pdb=" N LYS J 431 " pdb=" CA LYS J 431 " ideal model delta sigma weight residual 121.54 133.41 -11.87 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C ARG H 430 " pdb=" N LYS H 431 " pdb=" CA LYS H 431 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.86e+01 angle pdb=" N ILE J 397 " pdb=" CA ILE J 397 " pdb=" C ILE J 397 " ideal model delta sigma weight residual 111.67 106.00 5.67 9.50e-01 1.11e+00 3.56e+01 ... (remaining 27819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.51: 12055 20.51 - 41.03: 576 41.03 - 61.54: 102 61.54 - 82.05: 63 82.05 - 102.56: 24 Dihedral angle restraints: 12820 sinusoidal: 5708 harmonic: 7112 Sorted by residual: dihedral pdb=" CA ARG G 430 " pdb=" C ARG G 430 " pdb=" N LYS G 431 " pdb=" CA LYS G 431 " ideal model delta harmonic sigma weight residual -180.00 -143.33 -36.67 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CA ARG H 430 " pdb=" C ARG H 430 " pdb=" N LYS H 431 " pdb=" CA LYS H 431 " ideal model delta harmonic sigma weight residual -180.00 -143.45 -36.55 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA ARG J 430 " pdb=" C ARG J 430 " pdb=" N LYS J 431 " pdb=" CA LYS J 431 " ideal model delta harmonic sigma weight residual -180.00 -143.50 -36.50 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 12817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1388 0.056 - 0.113: 1105 0.113 - 0.169: 483 0.169 - 0.225: 185 0.225 - 0.282: 35 Chirality restraints: 3196 Sorted by residual: chirality pdb=" C1 MAN Q 4 " pdb=" O3 BMA Q 3 " pdb=" C2 MAN Q 4 " pdb=" O5 MAN Q 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.93e+01 chirality pdb=" C1 MAN W 4 " pdb=" O3 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.67e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.11e+01 ... (remaining 3193 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " -0.088 2.00e-02 2.50e+03 7.60e-02 7.21e+01 pdb=" C7 NAG Q 1 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " -0.078 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " 0.107 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.087 2.00e-02 2.50e+03 7.54e-02 7.11e+01 pdb=" C7 NAG F 1 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.077 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.087 2.00e-02 2.50e+03 7.48e-02 7.00e+01 pdb=" C7 NAG W 1 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.076 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.001 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2596 2.79 - 3.31: 19147 3.31 - 3.84: 35950 3.84 - 4.37: 46110 4.37 - 4.90: 73522 Nonbonded interactions: 177325 Sorted by model distance: nonbonded pdb=" O ASP G 293 " pdb="CA CA G1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP I 293 " pdb="CA CA I1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP H 293 " pdb="CA CA H1103 " model vdw 2.257 2.510 nonbonded pdb=" O ASP J 293 " pdb="CA CA J1103 " model vdw 2.265 2.510 nonbonded pdb=" O GLY J 345 " pdb="CA CA J1103 " model vdw 2.323 2.510 ... (remaining 177320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'T' selection = chain 'W' } ncs_group { reference = (chain 'G' and (resid 82 through 469 or resid 1101 through 1103)) selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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 individual isotropic 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: 9.110 Set stop_for_unknowns flag: 0.020 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 47.860 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 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 : 0.014 0.079 20492 Z= 0.916 Angle : 1.611 11.913 27824 Z= 1.043 Chirality : 0.092 0.282 3196 Planarity : 0.010 0.076 3500 Dihedral : 14.337 102.563 8160 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.88 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.74 (0.16), residues: 2476 helix: 0.14 (0.94), residues: 24 sheet: 0.03 (0.16), residues: 1012 loop : -0.88 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.016 TRP H 458 HIS 0.024 0.006 HIS H 168 PHE 0.066 0.012 PHE G 205 TYR 0.060 0.013 TYR H 281 ARG 0.020 0.003 ARG G 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 2.397 Fit side-chains REVERT: G 400 ARG cc_start: 0.8987 (ptm-80) cc_final: 0.8568 (ptm160) REVERT: G 467 MET cc_start: 0.9081 (ptm) cc_final: 0.8878 (ptm) REVERT: A 10 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8503 (mt-10) REVERT: A 62 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8282 (tp-100) REVERT: L 61 ARG cc_start: 0.9078 (ptt-90) cc_final: 0.8828 (ptt-90) REVERT: L 82 ASP cc_start: 0.9266 (m-30) cc_final: 0.9047 (m-30) REVERT: H 400 ARG cc_start: 0.8991 (ptm-80) cc_final: 0.8573 (ptm160) REVERT: B 10 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8498 (mt-10) REVERT: B 62 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8268 (tp-100) REVERT: M 61 ARG cc_start: 0.9084 (ptt-90) cc_final: 0.8832 (ptt-90) REVERT: M 82 ASP cc_start: 0.9269 (m-30) cc_final: 0.9049 (m-30) REVERT: I 400 ARG cc_start: 0.8955 (ptm-80) cc_final: 0.8558 (ptm160) REVERT: C 10 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8497 (mt-10) REVERT: C 62 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8283 (tp-100) REVERT: N 61 ARG cc_start: 0.9081 (ptt-90) cc_final: 0.8831 (ptt-90) REVERT: N 82 ASP cc_start: 0.9267 (m-30) cc_final: 0.9046 (m-30) REVERT: J 247 THR cc_start: 0.7304 (m) cc_final: 0.6837 (p) REVERT: J 400 ARG cc_start: 0.8955 (ptm-80) cc_final: 0.8559 (ptm160) REVERT: D 10 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8501 (mt-10) REVERT: D 62 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8331 (tp-100) REVERT: O 61 ARG cc_start: 0.9085 (ptt-90) cc_final: 0.8826 (ptt-90) REVERT: O 82 ASP cc_start: 0.9270 (m-30) cc_final: 0.9045 (m-30) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 1.4863 time to fit residues: 551.6238 Evaluate side-chains 277 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS A 65 GLN L 6 GLN H 347 HIS B 65 GLN M 6 GLN I 347 HIS C 65 GLN N 6 GLN J 347 HIS O 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20492 Z= 0.235 Angle : 0.656 5.984 27824 Z= 0.360 Chirality : 0.048 0.155 3196 Planarity : 0.004 0.033 3500 Dihedral : 9.310 78.798 3848 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.42 % Favored : 97.25 % Rotamer: Outliers : 1.27 % Allowed : 8.68 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.01 (0.16), residues: 2476 helix: -0.43 (0.84), residues: 24 sheet: 0.24 (0.15), residues: 1080 loop : -0.10 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 178 HIS 0.005 0.001 HIS J 347 PHE 0.013 0.002 PHE J 410 TYR 0.014 0.002 TYR J 121 ARG 0.003 0.001 ARG I 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 277 time to evaluate : 2.182 Fit side-chains REVERT: G 400 ARG cc_start: 0.8818 (ptm-80) cc_final: 0.8422 (ptm160) REVERT: A 62 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8196 (tp-100) REVERT: L 61 ARG cc_start: 0.9148 (ptt-90) cc_final: 0.8846 (ptt-90) REVERT: L 82 ASP cc_start: 0.9278 (m-30) cc_final: 0.9025 (m-30) REVERT: L 101 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8611 (mm110) REVERT: H 400 ARG cc_start: 0.8826 (ptm-80) cc_final: 0.8426 (ptm160) REVERT: B 62 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8217 (tp-100) REVERT: M 61 ARG cc_start: 0.9150 (ptt-90) cc_final: 0.8845 (ptt-90) REVERT: M 82 ASP cc_start: 0.9277 (m-30) cc_final: 0.9023 (m-30) REVERT: M 101 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8612 (mm110) REVERT: I 400 ARG cc_start: 0.8803 (ptm-80) cc_final: 0.8434 (ptm160) REVERT: C 62 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8198 (tp-100) REVERT: N 61 ARG cc_start: 0.9151 (ptt-90) cc_final: 0.8846 (ptt-90) REVERT: N 82 ASP cc_start: 0.9277 (m-30) cc_final: 0.9025 (m-30) REVERT: N 101 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8613 (mm110) REVERT: J 400 ARG cc_start: 0.8802 (ptm-80) cc_final: 0.8432 (ptm160) REVERT: D 62 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8315 (mm-40) REVERT: O 61 ARG cc_start: 0.9142 (ptt-90) cc_final: 0.8840 (ptt-90) REVERT: O 82 ASP cc_start: 0.9281 (m-30) cc_final: 0.9027 (m-30) REVERT: O 101 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8601 (mm110) outliers start: 27 outliers final: 8 residues processed: 285 average time/residue: 1.4326 time to fit residues: 458.1270 Evaluate side-chains 264 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 256 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 0.0770 chunk 194 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 65 GLN L 6 GLN B 65 GLN M 6 GLN C 30 ASN C 65 GLN N 6 GLN J 141 ASN D 30 ASN O 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20492 Z= 0.223 Angle : 0.592 6.480 27824 Z= 0.320 Chirality : 0.046 0.172 3196 Planarity : 0.003 0.039 3500 Dihedral : 8.217 67.397 3848 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.83 % Favored : 96.85 % Rotamer: Outliers : 1.84 % Allowed : 9.95 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.13 (0.17), residues: 2476 helix: 0.21 (0.91), residues: 24 sheet: 0.36 (0.15), residues: 1080 loop : -0.05 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 178 HIS 0.003 0.001 HIS H 274 PHE 0.012 0.002 PHE G 354 TYR 0.014 0.001 TYR H 121 ARG 0.003 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 261 time to evaluate : 2.263 Fit side-chains REVERT: G 400 ARG cc_start: 0.8841 (ptm-80) cc_final: 0.8400 (ptm160) REVERT: A 62 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8174 (tp-100) REVERT: L 61 ARG cc_start: 0.9107 (ptt-90) cc_final: 0.8814 (ptt-90) REVERT: H 400 ARG cc_start: 0.8831 (ptm-80) cc_final: 0.8388 (ptm160) REVERT: B 62 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8155 (tp-100) REVERT: M 61 ARG cc_start: 0.9109 (ptt-90) cc_final: 0.8814 (ptt-90) REVERT: I 400 ARG cc_start: 0.8817 (ptm-80) cc_final: 0.8391 (ptm160) REVERT: C 62 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8175 (tp-100) REVERT: N 61 ARG cc_start: 0.9116 (ptt-90) cc_final: 0.8822 (ptt-90) REVERT: J 400 ARG cc_start: 0.8815 (ptm-80) cc_final: 0.8393 (ptm160) REVERT: D 62 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8306 (tp-100) REVERT: O 61 ARG cc_start: 0.9104 (ptt-90) cc_final: 0.8815 (ptt-90) REVERT: O 101 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8731 (mm110) outliers start: 39 outliers final: 19 residues processed: 282 average time/residue: 1.3027 time to fit residues: 416.1631 Evaluate side-chains 268 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 249 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 30 ASN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20492 Z= 0.402 Angle : 0.646 6.976 27824 Z= 0.349 Chirality : 0.049 0.183 3196 Planarity : 0.004 0.043 3500 Dihedral : 8.552 70.774 3848 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.07 % Favored : 96.61 % Rotamer: Outliers : 1.79 % Allowed : 10.24 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.04 (0.16), residues: 2476 helix: 0.35 (0.91), residues: 24 sheet: 0.31 (0.15), residues: 1004 loop : -0.10 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 115 HIS 0.004 0.001 HIS H 168 PHE 0.014 0.002 PHE G 410 TYR 0.015 0.002 TYR H 121 ARG 0.003 0.000 ARG H 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 251 time to evaluate : 2.379 Fit side-chains REVERT: G 400 ARG cc_start: 0.8936 (ptm-80) cc_final: 0.8464 (ptm160) REVERT: A 62 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8255 (tp-100) REVERT: L 61 ARG cc_start: 0.9109 (ptt-90) cc_final: 0.8720 (ptt-90) REVERT: H 400 ARG cc_start: 0.8939 (ptm-80) cc_final: 0.8467 (ptm160) REVERT: B 62 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8254 (tp-100) REVERT: M 61 ARG cc_start: 0.9110 (ptt-90) cc_final: 0.8722 (ptt-90) REVERT: I 400 ARG cc_start: 0.8928 (ptm-80) cc_final: 0.8456 (ptm160) REVERT: C 62 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8255 (tp-100) REVERT: N 61 ARG cc_start: 0.9110 (ptt-90) cc_final: 0.8723 (ptt-90) REVERT: J 400 ARG cc_start: 0.8929 (ptm-80) cc_final: 0.8456 (ptm160) REVERT: D 62 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8339 (tp-100) REVERT: O 61 ARG cc_start: 0.9126 (ptt-90) cc_final: 0.8736 (ptt-90) outliers start: 38 outliers final: 33 residues processed: 268 average time/residue: 1.2934 time to fit residues: 393.0629 Evaluate side-chains 279 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 246 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 308 LYS Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 30 ASN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20492 Z= 0.345 Angle : 0.623 7.962 27824 Z= 0.335 Chirality : 0.047 0.175 3196 Planarity : 0.004 0.043 3500 Dihedral : 8.379 68.921 3848 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.50 % Favored : 97.17 % Rotamer: Outliers : 1.84 % Allowed : 10.33 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.01 (0.16), residues: 2476 helix: 0.37 (0.90), residues: 24 sheet: 0.25 (0.15), residues: 1008 loop : -0.09 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 178 HIS 0.003 0.001 HIS G 184 PHE 0.014 0.002 PHE H 410 TYR 0.013 0.002 TYR J 121 ARG 0.003 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 251 time to evaluate : 2.163 Fit side-chains REVERT: G 400 ARG cc_start: 0.8947 (ptm-80) cc_final: 0.8444 (ptm160) REVERT: A 62 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8188 (tp-100) REVERT: L 61 ARG cc_start: 0.9103 (ptt-90) cc_final: 0.8677 (ptt-90) REVERT: H 400 ARG cc_start: 0.8950 (ptm-80) cc_final: 0.8445 (ptm160) REVERT: B 62 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8220 (tp-100) REVERT: M 61 ARG cc_start: 0.9104 (ptt-90) cc_final: 0.8679 (ptt-90) REVERT: I 400 ARG cc_start: 0.8932 (ptm-80) cc_final: 0.8433 (ptm160) REVERT: C 62 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8187 (tp-100) REVERT: N 61 ARG cc_start: 0.9103 (ptt-90) cc_final: 0.8678 (ptt-90) REVERT: J 400 ARG cc_start: 0.8932 (ptm-80) cc_final: 0.8433 (ptm160) REVERT: D 62 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8291 (tp-100) REVERT: O 61 ARG cc_start: 0.9097 (ptt-90) cc_final: 0.8666 (ptt-90) REVERT: O 104 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8604 (tttp) outliers start: 39 outliers final: 32 residues processed: 271 average time/residue: 1.4112 time to fit residues: 432.5081 Evaluate side-chains 281 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 248 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 104 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 0.0170 chunk 121 optimal weight: 0.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20492 Z= 0.173 Angle : 0.561 8.535 27824 Z= 0.300 Chirality : 0.045 0.184 3196 Planarity : 0.003 0.042 3500 Dihedral : 7.500 59.463 3848 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.63 % Favored : 97.17 % Rotamer: Outliers : 1.65 % Allowed : 10.94 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.02 (0.16), residues: 2476 helix: -0.54 (0.84), residues: 28 sheet: 0.22 (0.15), residues: 1032 loop : -0.03 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 178 HIS 0.002 0.001 HIS J 274 PHE 0.012 0.002 PHE G 410 TYR 0.012 0.001 TYR H 121 ARG 0.002 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 257 time to evaluate : 2.184 Fit side-chains REVERT: G 230 CYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8877 (p) REVERT: G 400 ARG cc_start: 0.8879 (ptm-80) cc_final: 0.8380 (ptm160) REVERT: A 62 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8151 (tp-100) REVERT: A 89 GLU cc_start: 0.9281 (pm20) cc_final: 0.9074 (pm20) REVERT: L 61 ARG cc_start: 0.9061 (ptt-90) cc_final: 0.8693 (ptt-90) REVERT: H 230 CYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8878 (p) REVERT: H 400 ARG cc_start: 0.8873 (ptm-80) cc_final: 0.8374 (ptm160) REVERT: B 62 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8161 (tp-100) REVERT: M 61 ARG cc_start: 0.9060 (ptt-90) cc_final: 0.8690 (ptt-90) REVERT: I 230 CYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8877 (p) REVERT: I 400 ARG cc_start: 0.8860 (ptm-80) cc_final: 0.8369 (ptm160) REVERT: C 62 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8151 (tp-100) REVERT: N 61 ARG cc_start: 0.9060 (ptt-90) cc_final: 0.8691 (ptt-90) REVERT: J 230 CYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8877 (p) REVERT: J 400 ARG cc_start: 0.8863 (ptm-80) cc_final: 0.8372 (ptm160) REVERT: D 62 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8287 (tp-100) REVERT: O 61 ARG cc_start: 0.9060 (ptt-90) cc_final: 0.8803 (ptt-90) outliers start: 35 outliers final: 11 residues processed: 271 average time/residue: 1.3450 time to fit residues: 410.6647 Evaluate side-chains 264 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain I residue 230 CYS Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 0.0970 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20492 Z= 0.174 Angle : 0.564 8.201 27824 Z= 0.299 Chirality : 0.045 0.199 3196 Planarity : 0.003 0.043 3500 Dihedral : 7.160 55.179 3848 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 1.04 % Allowed : 12.74 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: 0.03 (0.16), residues: 2476 helix: -1.80 (0.60), residues: 52 sheet: 0.33 (0.15), residues: 1024 loop : -0.04 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 178 HIS 0.002 0.001 HIS G 274 PHE 0.014 0.002 PHE L 83 TYR 0.012 0.001 TYR H 121 ARG 0.005 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 258 time to evaluate : 2.209 Fit side-chains REVERT: G 400 ARG cc_start: 0.8875 (ptm-80) cc_final: 0.8371 (ptm160) REVERT: A 62 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8157 (tp-100) REVERT: A 82 GLU cc_start: 0.8665 (tt0) cc_final: 0.8377 (mm-30) REVERT: L 61 ARG cc_start: 0.9054 (ptt-90) cc_final: 0.8812 (ptt-90) REVERT: H 400 ARG cc_start: 0.8874 (ptm-80) cc_final: 0.8372 (ptm160) REVERT: B 62 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8163 (tp-100) REVERT: B 82 GLU cc_start: 0.8679 (tt0) cc_final: 0.8381 (mm-30) REVERT: M 61 ARG cc_start: 0.9052 (ptt-90) cc_final: 0.8815 (ptt-90) REVERT: I 400 ARG cc_start: 0.8864 (ptm-80) cc_final: 0.8366 (ptm160) REVERT: C 62 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8158 (tp-100) REVERT: C 82 GLU cc_start: 0.8676 (tt0) cc_final: 0.8394 (mm-30) REVERT: N 61 ARG cc_start: 0.9053 (ptt-90) cc_final: 0.8816 (ptt-90) REVERT: J 400 ARG cc_start: 0.8865 (ptm-80) cc_final: 0.8368 (ptm160) REVERT: D 62 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8292 (tp-100) REVERT: D 82 GLU cc_start: 0.8688 (tt0) cc_final: 0.8387 (mm-30) REVERT: O 61 ARG cc_start: 0.9062 (ptt-90) cc_final: 0.8812 (ptt-90) outliers start: 22 outliers final: 12 residues processed: 273 average time/residue: 1.3365 time to fit residues: 412.1073 Evaluate side-chains 264 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 252 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 220 ASN A 65 GLN L 6 GLN L 70 GLN H 220 ASN B 65 GLN M 6 GLN M 70 GLN I 220 ASN C 65 GLN N 6 GLN N 70 GLN J 220 ASN O 6 GLN O 70 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20492 Z= 0.255 Angle : 0.598 8.042 27824 Z= 0.317 Chirality : 0.046 0.207 3196 Planarity : 0.004 0.043 3500 Dihedral : 7.365 57.135 3848 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 0.90 % Allowed : 13.02 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.03 (0.16), residues: 2476 helix: -1.79 (0.60), residues: 52 sheet: 0.31 (0.16), residues: 940 loop : -0.09 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 178 HIS 0.002 0.001 HIS J 184 PHE 0.013 0.002 PHE G 410 TYR 0.013 0.001 TYR G 121 ARG 0.005 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 253 time to evaluate : 2.058 Fit side-chains REVERT: G 400 ARG cc_start: 0.8912 (ptm-80) cc_final: 0.8392 (ptm160) REVERT: A 62 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8205 (tp-100) REVERT: A 82 GLU cc_start: 0.8683 (tt0) cc_final: 0.8419 (mm-30) REVERT: L 61 ARG cc_start: 0.9051 (ptt-90) cc_final: 0.8788 (ptt-90) REVERT: H 400 ARG cc_start: 0.8911 (ptm-80) cc_final: 0.8389 (ptm160) REVERT: B 62 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8200 (tp-100) REVERT: B 82 GLU cc_start: 0.8709 (tt0) cc_final: 0.8404 (mm-30) REVERT: M 61 ARG cc_start: 0.9050 (ptt-90) cc_final: 0.8790 (ptt-90) REVERT: I 400 ARG cc_start: 0.8904 (ptm-80) cc_final: 0.8390 (ptm160) REVERT: C 62 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8204 (tp-100) REVERT: C 82 GLU cc_start: 0.8685 (tt0) cc_final: 0.8421 (mm-30) REVERT: N 61 ARG cc_start: 0.9043 (ptt-90) cc_final: 0.8765 (ptt-90) REVERT: J 400 ARG cc_start: 0.8908 (ptm-80) cc_final: 0.8392 (ptm160) REVERT: D 62 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8346 (tp-100) REVERT: D 82 GLU cc_start: 0.8706 (tt0) cc_final: 0.8395 (mm-30) REVERT: O 61 ARG cc_start: 0.9047 (ptt-90) cc_final: 0.8758 (ptt-90) outliers start: 19 outliers final: 18 residues processed: 264 average time/residue: 1.3389 time to fit residues: 398.8954 Evaluate side-chains 269 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 251 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 0.0670 chunk 66 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20492 Z= 0.191 Angle : 0.568 8.227 27824 Z= 0.301 Chirality : 0.045 0.203 3196 Planarity : 0.003 0.043 3500 Dihedral : 7.087 53.708 3848 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 0.94 % Allowed : 13.44 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.02 (0.16), residues: 2476 helix: -1.78 (0.60), residues: 52 sheet: 0.36 (0.16), residues: 948 loop : -0.11 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 178 HIS 0.002 0.001 HIS H 274 PHE 0.013 0.002 PHE L 83 TYR 0.012 0.001 TYR H 121 ARG 0.004 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 261 time to evaluate : 2.255 Fit side-chains REVERT: G 400 ARG cc_start: 0.8884 (ptm-80) cc_final: 0.8366 (ptm160) REVERT: A 62 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8180 (tp-100) REVERT: A 82 GLU cc_start: 0.8755 (tt0) cc_final: 0.8404 (mm-30) REVERT: L 61 ARG cc_start: 0.9044 (ptt-90) cc_final: 0.8798 (ptt-90) REVERT: H 400 ARG cc_start: 0.8887 (ptm-80) cc_final: 0.8372 (ptm160) REVERT: B 62 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8189 (tp-100) REVERT: B 82 GLU cc_start: 0.8670 (tt0) cc_final: 0.8403 (mm-30) REVERT: M 61 ARG cc_start: 0.9034 (ptt-90) cc_final: 0.8765 (ptt-90) REVERT: I 400 ARG cc_start: 0.8874 (ptm-80) cc_final: 0.8364 (ptm160) REVERT: C 62 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8184 (tp-100) REVERT: C 82 GLU cc_start: 0.8756 (tt0) cc_final: 0.8390 (mm-30) REVERT: N 61 ARG cc_start: 0.9033 (ptt-90) cc_final: 0.8765 (ptt-90) REVERT: J 400 ARG cc_start: 0.8878 (ptm-80) cc_final: 0.8366 (ptm160) REVERT: D 62 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8331 (tp-100) REVERT: D 82 GLU cc_start: 0.8656 (tt0) cc_final: 0.8389 (mm-30) REVERT: O 61 ARG cc_start: 0.9032 (ptt-90) cc_final: 0.8751 (ptt-90) REVERT: O 104 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8517 (tmtm) outliers start: 20 outliers final: 19 residues processed: 273 average time/residue: 1.3928 time to fit residues: 427.6835 Evaluate side-chains 275 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 255 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 104 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN M 70 GLN C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20492 Z= 0.242 Angle : 0.589 8.076 27824 Z= 0.312 Chirality : 0.046 0.209 3196 Planarity : 0.003 0.043 3500 Dihedral : 7.206 54.899 3848 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.87 % Favored : 96.97 % Rotamer: Outliers : 1.04 % Allowed : 13.77 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.04 (0.16), residues: 2476 helix: -1.81 (0.60), residues: 52 sheet: 0.32 (0.16), residues: 948 loop : -0.12 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 178 HIS 0.002 0.001 HIS I 184 PHE 0.014 0.002 PHE L 83 TYR 0.013 0.001 TYR H 121 ARG 0.005 0.000 ARG C 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 250 time to evaluate : 2.365 Fit side-chains REVERT: G 400 ARG cc_start: 0.8908 (ptm-80) cc_final: 0.8382 (ptm160) REVERT: A 62 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8211 (tp-100) REVERT: A 82 GLU cc_start: 0.8686 (tt0) cc_final: 0.8432 (mm-30) REVERT: L 61 ARG cc_start: 0.9030 (ptt-90) cc_final: 0.8756 (ptt-90) REVERT: H 400 ARG cc_start: 0.8908 (ptm-80) cc_final: 0.8384 (ptm160) REVERT: B 62 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8213 (tp-100) REVERT: B 82 GLU cc_start: 0.8763 (tt0) cc_final: 0.8411 (mm-30) REVERT: M 61 ARG cc_start: 0.9029 (ptt-90) cc_final: 0.8748 (ptt-90) REVERT: M 104 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8518 (tmtm) REVERT: I 400 ARG cc_start: 0.8902 (ptm-80) cc_final: 0.8377 (ptm160) REVERT: C 62 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8212 (tp-100) REVERT: C 82 GLU cc_start: 0.8686 (tt0) cc_final: 0.8433 (mm-30) REVERT: N 61 ARG cc_start: 0.9029 (ptt-90) cc_final: 0.8747 (ptt-90) REVERT: N 104 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8518 (tmtm) REVERT: J 400 ARG cc_start: 0.8904 (ptm-80) cc_final: 0.8379 (ptm160) REVERT: D 62 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8346 (tp-100) REVERT: D 82 GLU cc_start: 0.8769 (tt0) cc_final: 0.8437 (mm-30) REVERT: O 61 ARG cc_start: 0.9033 (ptt-90) cc_final: 0.8741 (ptt-90) REVERT: O 104 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8518 (tmtm) outliers start: 22 outliers final: 19 residues processed: 264 average time/residue: 1.3502 time to fit residues: 401.7157 Evaluate side-chains 271 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 467 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 467 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 104 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN L 6 GLN L 70 GLN B 65 GLN M 6 GLN ** M 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN N 6 GLN N 70 GLN O 6 GLN O 70 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.069718 restraints weight = 28117.060| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.19 r_work: 0.2714 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20492 Z= 0.251 Angle : 0.591 8.072 27824 Z= 0.314 Chirality : 0.046 0.203 3196 Planarity : 0.003 0.043 3500 Dihedral : 7.270 55.645 3848 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 1.08 % Allowed : 13.82 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % 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: -0.04 (0.16), residues: 2476 helix: -1.83 (0.59), residues: 52 sheet: 0.32 (0.16), residues: 948 loop : -0.11 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 178 HIS 0.002 0.001 HIS J 184 PHE 0.013 0.002 PHE J 410 TYR 0.012 0.001 TYR G 121 ARG 0.005 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7427.24 seconds wall clock time: 131 minutes 22.41 seconds (7882.41 seconds total)