Starting phenix.real_space_refine on Tue Oct 15 05:25:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsn_24675/10_2024/7rsn_24675.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsn_24675/10_2024/7rsn_24675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsn_24675/10_2024/7rsn_24675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsn_24675/10_2024/7rsn_24675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsn_24675/10_2024/7rsn_24675.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsn_24675/10_2024/7rsn_24675.cif" } resolution = 3.49 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= 0.002 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 12333 2.51 5 N 3267 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 19623 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3344 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 4 Chain: "B" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 995 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "C" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3344 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 4 Chain: "D" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 995 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "G" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3344 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 4 Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 995 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 93} Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 93} Chain: "F" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "K" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 93} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 11.66, per 1000 atoms: 0.59 Number of scatterers: 19623 At special positions: 0 Unit cell: (148.03, 138.86, 120.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 3900 8.00 N 3267 7.00 C 12333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.07 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.07 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.02 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.07 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 N 4 " - " MAN N 5 " " MAN T 4 " - " MAN T 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 4 " - " MAN Q 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA W 3 " - " MAN W 6 " " MAN W 4 " - " MAN W 5 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA c 3 " - " MAN c 6 " " MAN c 4 " - " MAN c 5 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 6 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 6 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 6 " " BMA c 3 " - " MAN c 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG 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 S 2 " - " BMA S 3 " " 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 Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 463 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 392 " " NAG A 604 " - " ASN A 332 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 230 " " NAG A 609 " - " ASN A 130 " " NAG A 610 " - " ASN A 355 " " NAG C 601 " - " ASN C 463 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 332 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 230 " " NAG C 609 " - " ASN C 130 " " NAG C 610 " - " ASN C 355 " " NAG G 601 " - " ASN G 463 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 392 " " NAG G 604 " - " ASN G 332 " " NAG G 605 " - " ASN G 295 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 448 " " NAG G 608 " - " ASN G 230 " " NAG G 609 " - " ASN G 130 " " NAG G 610 " - " ASN G 355 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 197 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 241 " " NAG S 1 " - " ASN C 276 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 386 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 241 " " NAG Y 1 " - " ASN G 276 " " NAG Z 1 " - " ASN G 197 " " NAG a 1 " - " ASN G 386 " " NAG b 1 " - " ASN G 156 " " NAG c 1 " - " ASN G 262 " " NAG d 1 " - " ASN G 241 " Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 2.4 seconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4284 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 20.1% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.621A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.568A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 removed outlier: 3.997A pdb=" N ALA B 533 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.550A pdb=" N GLN B 540 " --> pdb=" O ALA B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 594 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.804A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 664 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.621A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.568A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 535 removed outlier: 3.998A pdb=" N ALA D 533 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.550A pdb=" N GLN D 540 " --> pdb=" O ALA D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 594 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.805A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 664 Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.620A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.568A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 530 through 535 removed outlier: 3.998A pdb=" N ALA I 533 " --> pdb=" O MET I 530 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N MET I 535 " --> pdb=" O ALA I 532 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.550A pdb=" N GLN I 540 " --> pdb=" O ALA I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 594 Processing helix chain 'I' and resid 618 through 622 Processing helix chain 'I' and resid 627 through 635 removed outlier: 3.804A pdb=" N ILE I 635 " --> pdb=" O TRP I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 645 through 664 Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 60 through 65 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 60 through 65 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.051A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.509A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.779A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.284A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.050A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.508A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.779A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.284A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 494 through 498 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'G' and resid 169 through 176 Processing sheet with id=AC6, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.050A pdb=" N VAL G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR G 435 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 259 through 261 removed outlier: 3.509A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.780A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE G 468 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.284A pdb=" N ARG G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 8.111A pdb=" N GLU H 33 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS H 52 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE H 35 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.340A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.147A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.147A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'E' and resid 10 through 12 removed outlier: 8.111A pdb=" N GLU E 33 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS E 52 " --> pdb=" O GLU E 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 35 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP E 50 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.340A pdb=" N LEU E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.147A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.147A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'F' and resid 10 through 12 removed outlier: 8.111A pdb=" N GLU F 33 " --> pdb=" O LYS F 52 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS F 52 " --> pdb=" O GLU F 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE F 35 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP F 50 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.340A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.148A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.148A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1890 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: 8.13 Time building geometry restraints manager: 6.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3721 1.32 - 1.45: 6278 1.45 - 1.59: 9770 1.59 - 1.72: 91 1.72 - 1.86: 165 Bond restraints: 20025 Sorted by residual: bond pdb=" CA SER A 132 " pdb=" C SER A 132 " ideal model delta sigma weight residual 1.520 1.568 -0.048 4.80e-03 4.34e+04 1.01e+02 bond pdb=" CA SER C 132 " pdb=" C SER C 132 " ideal model delta sigma weight residual 1.520 1.568 -0.048 4.80e-03 4.34e+04 1.00e+02 bond pdb=" CA SER G 132 " pdb=" C SER G 132 " ideal model delta sigma weight residual 1.520 1.568 -0.048 4.80e-03 4.34e+04 9.99e+01 bond pdb=" NE ARG G 504 " pdb=" CZ ARG G 504 " ideal model delta sigma weight residual 1.326 1.408 -0.082 1.10e-02 8.26e+03 5.53e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.408 -0.082 1.10e-02 8.26e+03 5.52e+01 ... (remaining 20020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.11: 27069 7.11 - 14.22: 90 14.22 - 21.33: 3 21.33 - 28.43: 0 28.43 - 35.54: 3 Bond angle restraints: 27165 Sorted by residual: angle pdb=" N PRO C 76 " pdb=" CA PRO C 76 " pdb=" C PRO C 76 " ideal model delta sigma weight residual 111.14 91.67 19.47 1.56e+00 4.11e-01 1.56e+02 angle pdb=" N PRO A 76 " pdb=" CA PRO A 76 " pdb=" C PRO A 76 " ideal model delta sigma weight residual 111.14 91.68 19.46 1.56e+00 4.11e-01 1.56e+02 angle pdb=" N PRO G 76 " pdb=" CA PRO G 76 " pdb=" C PRO G 76 " ideal model delta sigma weight residual 111.14 91.68 19.46 1.56e+00 4.11e-01 1.56e+02 angle pdb=" C2 NAG T 1 " pdb=" N2 NAG T 1 " pdb=" C7 NAG T 1 " ideal model delta sigma weight residual 124.56 160.10 -35.54 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG N 1 " pdb=" N2 NAG N 1 " pdb=" C7 NAG N 1 " ideal model delta sigma weight residual 124.56 160.08 -35.52 3.00e+00 1.11e-01 1.40e+02 ... (remaining 27160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 12768 21.12 - 42.24: 279 42.24 - 63.36: 78 63.36 - 84.48: 81 84.48 - 105.61: 48 Dihedral angle restraints: 13254 sinusoidal: 6621 harmonic: 6633 Sorted by residual: dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual -86.00 -172.70 86.70 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -172.69 86.69 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -172.67 86.67 1 1.00e+01 1.00e-02 9.04e+01 ... (remaining 13251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2401 0.124 - 0.247: 602 0.247 - 0.371: 240 0.371 - 0.495: 69 0.495 - 0.618: 6 Chirality restraints: 3318 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.41e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.38e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 ... (remaining 3315 not shown) Planarity restraints: 3357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 230 " -0.095 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN C 230 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN C 230 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN C 230 " 0.156 2.00e-02 2.50e+03 pdb=" C1 NAG C 608 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 230 " 0.095 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN A 230 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 230 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 230 " -0.156 2.00e-02 2.50e+03 pdb=" C1 NAG A 608 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 230 " 0.095 2.00e-02 2.50e+03 9.99e-02 1.25e+02 pdb=" CG ASN G 230 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN G 230 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN G 230 " -0.156 2.00e-02 2.50e+03 pdb=" C1 NAG G 608 " 0.122 2.00e-02 2.50e+03 ... (remaining 3354 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5001 2.82 - 3.34: 17496 3.34 - 3.86: 32091 3.86 - 4.38: 38694 4.38 - 4.90: 61517 Nonbonded interactions: 154799 Sorted by model distance: nonbonded pdb=" N PRO A 76 " pdb=" O PRO A 76 " model vdw 2.296 2.496 nonbonded pdb=" N PRO C 76 " pdb=" O PRO C 76 " model vdw 2.296 2.496 nonbonded pdb=" N PRO G 76 " pdb=" O PRO G 76 " model vdw 2.297 2.496 nonbonded pdb=" N ASN C 234 " pdb=" OD1 ASN C 234 " model vdw 2.440 3.120 nonbonded pdb=" N ASN G 234 " pdb=" OD1 ASN G 234 " model vdw 2.440 3.120 ... (remaining 154794 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 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'S' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'd' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 46.490 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.023 0.125 20025 Z= 1.448 Angle : 1.843 35.542 27165 Z= 1.176 Chirality : 0.138 0.618 3318 Planarity : 0.009 0.060 3309 Dihedral : 13.448 105.606 8862 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.99 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.94 % 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: 0.48 (0.17), residues: 2256 helix: 0.26 (0.23), residues: 354 sheet: 1.00 (0.19), residues: 735 loop : -0.01 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.011 TRP I 610 HIS 0.011 0.003 HIS K 32 PHE 0.032 0.006 PHE A 353 TYR 0.032 0.007 TYR A 318 ARG 0.006 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 632 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8863 (m-80) cc_final: 0.8331 (m-10) REVERT: A 217 TYR cc_start: 0.8840 (m-80) cc_final: 0.7367 (m-80) REVERT: B 650 GLN cc_start: 0.7695 (tp40) cc_final: 0.7270 (tm-30) REVERT: C 180 ASP cc_start: 0.7875 (m-30) cc_final: 0.7631 (m-30) REVERT: C 316 TRP cc_start: 0.7469 (p90) cc_final: 0.7126 (p90) REVERT: C 502 LYS cc_start: 0.8439 (tttt) cc_final: 0.8235 (mtpt) REVERT: G 191 TYR cc_start: 0.8856 (m-80) cc_final: 0.8240 (m-80) REVERT: G 217 TYR cc_start: 0.8853 (m-80) cc_final: 0.8360 (m-80) REVERT: L 42 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7830 (mm-40) REVERT: E 68 SER cc_start: 0.8916 (t) cc_final: 0.8626 (p) REVERT: J 42 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7638 (mm110) REVERT: F 68 SER cc_start: 0.8846 (t) cc_final: 0.8628 (p) REVERT: K 14 SER cc_start: 0.7452 (m) cc_final: 0.7125 (p) outliers start: 0 outliers final: 0 residues processed: 632 average time/residue: 0.3755 time to fit residues: 341.2833 Evaluate side-chains 298 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 203 GLN A 344 GLN B 590 GLN C 105 HIS C 114 GLN C 344 GLN C 377 ASN D 590 GLN G 105 HIS G 203 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS E 65 GLN E 79 HIS F 65 GLN F 79 HIS K 66 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20025 Z= 0.250 Angle : 0.793 18.222 27165 Z= 0.398 Chirality : 0.051 0.338 3318 Planarity : 0.005 0.056 3309 Dihedral : 10.805 76.756 4488 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 2.17 % Allowed : 8.58 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.41 (0.18), residues: 2256 helix: 1.63 (0.28), residues: 381 sheet: 0.44 (0.18), residues: 786 loop : -0.28 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 479 HIS 0.006 0.002 HIS A 105 PHE 0.018 0.002 PHE A 233 TYR 0.019 0.002 TYR J 86 ARG 0.007 0.001 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 398 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8633 (mtp85) cc_final: 0.8225 (ttm110) REVERT: A 191 TYR cc_start: 0.8813 (m-80) cc_final: 0.8557 (m-10) REVERT: A 217 TYR cc_start: 0.8842 (m-80) cc_final: 0.7470 (m-80) REVERT: B 535 MET cc_start: 0.7762 (mpp) cc_final: 0.7302 (mmm) REVERT: B 620 ASP cc_start: 0.6976 (p0) cc_final: 0.6774 (p0) REVERT: B 635 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.6052 (mt) REVERT: C 173 TYR cc_start: 0.8589 (m-80) cc_final: 0.8334 (m-80) REVERT: C 316 TRP cc_start: 0.7178 (p90) cc_final: 0.6834 (p90) REVERT: G 166 ARG cc_start: 0.8674 (mtp85) cc_final: 0.8379 (mtm180) REVERT: G 502 LYS cc_start: 0.8005 (tttm) cc_final: 0.7513 (mttp) REVERT: F 80 MET cc_start: 0.8518 (ttt) cc_final: 0.8310 (ttt) REVERT: F 96 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7910 (mtmm) outliers start: 44 outliers final: 23 residues processed: 422 average time/residue: 0.3322 time to fit residues: 210.7173 Evaluate side-chains 333 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 309 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN I 577 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 20025 Z= 0.453 Angle : 0.818 17.682 27165 Z= 0.411 Chirality : 0.052 0.264 3318 Planarity : 0.005 0.054 3309 Dihedral : 9.706 70.990 4488 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.27 % Favored : 94.46 % Rotamer: Outliers : 3.16 % Allowed : 9.17 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.18), residues: 2256 helix: 1.50 (0.28), residues: 378 sheet: 0.09 (0.17), residues: 834 loop : -0.78 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP G 112 HIS 0.006 0.003 HIS C 374 PHE 0.026 0.002 PHE A 376 TYR 0.020 0.002 TYR G 191 ARG 0.009 0.001 ARG L 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 378 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8691 (mtp85) cc_final: 0.8488 (mtp85) REVERT: A 191 TYR cc_start: 0.8871 (m-80) cc_final: 0.8606 (m-10) REVERT: B 651 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7164 (t0) REVERT: C 173 TYR cc_start: 0.8532 (m-80) cc_final: 0.8300 (m-80) REVERT: C 191 TYR cc_start: 0.8861 (m-80) cc_final: 0.8653 (m-80) REVERT: D 530 MET cc_start: 0.7164 (mtp) cc_final: 0.6907 (mtp) REVERT: G 166 ARG cc_start: 0.8762 (mtp85) cc_final: 0.8148 (mtm180) REVERT: G 191 TYR cc_start: 0.8685 (m-80) cc_final: 0.8484 (m-80) REVERT: I 615 SER cc_start: 0.6938 (t) cc_final: 0.6663 (p) REVERT: K 37 GLN cc_start: 0.8388 (tt0) cc_final: 0.8146 (tt0) outliers start: 64 outliers final: 45 residues processed: 408 average time/residue: 0.3457 time to fit residues: 209.9345 Evaluate side-chains 376 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 330 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 78 MET Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 220 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN C 377 ASN D 590 GLN G 377 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20025 Z= 0.197 Angle : 0.656 13.984 27165 Z= 0.322 Chirality : 0.048 0.250 3318 Planarity : 0.005 0.064 3309 Dihedral : 8.582 64.059 4488 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.52 % Favored : 95.17 % Rotamer: Outliers : 1.97 % Allowed : 11.69 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -0.14 (0.18), residues: 2256 helix: 1.62 (0.27), residues: 396 sheet: 0.05 (0.17), residues: 837 loop : -0.86 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 50 HIS 0.004 0.001 HIS L 32 PHE 0.018 0.002 PHE C 376 TYR 0.013 0.001 TYR J 86 ARG 0.006 0.001 ARG C 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 373 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8793 (m-80) cc_final: 0.8556 (m-80) REVERT: A 217 TYR cc_start: 0.8887 (m-80) cc_final: 0.7682 (m-80) REVERT: B 620 ASP cc_start: 0.7631 (p0) cc_final: 0.6971 (p0) REVERT: C 173 TYR cc_start: 0.8468 (m-80) cc_final: 0.8237 (m-80) REVERT: C 191 TYR cc_start: 0.8807 (m-80) cc_final: 0.8585 (m-80) REVERT: G 166 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8048 (mtp85) REVERT: I 615 SER cc_start: 0.6807 (t) cc_final: 0.6563 (p) REVERT: J 33 MET cc_start: 0.8328 (tpp) cc_final: 0.8101 (tpp) REVERT: F 62 ASP cc_start: 0.7844 (t0) cc_final: 0.7617 (t0) REVERT: K 37 GLN cc_start: 0.8376 (tt0) cc_final: 0.7970 (tt0) outliers start: 40 outliers final: 24 residues processed: 391 average time/residue: 0.3421 time to fit residues: 201.4841 Evaluate side-chains 344 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 320 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 3 optimal weight: 0.0020 chunk 164 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 overall best weight: 2.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100BGLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20025 Z= 0.415 Angle : 0.738 13.349 27165 Z= 0.368 Chirality : 0.050 0.267 3318 Planarity : 0.005 0.058 3309 Dihedral : 8.514 62.668 4488 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.32 % Favored : 94.28 % Rotamer: Outliers : 2.96 % Allowed : 12.13 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.39 (0.18), residues: 2256 helix: 1.71 (0.28), residues: 381 sheet: -0.02 (0.18), residues: 801 loop : -1.16 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 23 HIS 0.007 0.002 HIS A 374 PHE 0.023 0.002 PHE C 376 TYR 0.021 0.002 TYR G 191 ARG 0.008 0.001 ARG G 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 343 time to evaluate : 2.253 Fit side-chains revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8820 (m-80) cc_final: 0.8568 (m-80) REVERT: C 173 TYR cc_start: 0.8469 (m-80) cc_final: 0.8260 (m-80) REVERT: C 191 TYR cc_start: 0.8798 (m-80) cc_final: 0.8549 (m-10) REVERT: C 316 TRP cc_start: 0.7502 (OUTLIER) cc_final: 0.6685 (p90) REVERT: G 166 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8113 (mtp85) REVERT: E 62 ASP cc_start: 0.8376 (t0) cc_final: 0.7864 (t0) REVERT: J 33 MET cc_start: 0.8398 (tpp) cc_final: 0.8190 (tpp) REVERT: F 62 ASP cc_start: 0.8276 (t0) cc_final: 0.8039 (t0) REVERT: K 37 GLN cc_start: 0.8479 (tt0) cc_final: 0.8063 (tt0) outliers start: 60 outliers final: 46 residues processed: 371 average time/residue: 0.3547 time to fit residues: 195.9711 Evaluate side-chains 373 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 326 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.0870 chunk 198 optimal weight: 1.9990 chunk 43 optimal weight: 0.0000 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 ASN G 343 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20025 Z= 0.184 Angle : 0.630 10.873 27165 Z= 0.310 Chirality : 0.047 0.242 3318 Planarity : 0.005 0.067 3309 Dihedral : 7.863 58.467 4488 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.96 % Favored : 94.77 % Rotamer: Outliers : 2.02 % Allowed : 13.71 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2256 helix: 1.91 (0.28), residues: 381 sheet: 0.03 (0.18), residues: 822 loop : -1.14 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 50 HIS 0.005 0.001 HIS L 32 PHE 0.016 0.001 PHE C 376 TYR 0.015 0.001 TYR G 191 ARG 0.008 0.000 ARG J 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 356 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7026 (mm-30) REVERT: A 112 TRP cc_start: 0.8067 (t-100) cc_final: 0.7851 (t-100) REVERT: A 191 TYR cc_start: 0.8772 (m-80) cc_final: 0.8515 (m-80) REVERT: C 69 TRP cc_start: 0.7696 (m-90) cc_final: 0.7456 (m-90) REVERT: C 97 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.8047 (mmm-85) REVERT: C 173 TYR cc_start: 0.8443 (m-80) cc_final: 0.8215 (m-80) REVERT: C 191 TYR cc_start: 0.8804 (m-80) cc_final: 0.8573 (m-80) REVERT: C 316 TRP cc_start: 0.7332 (OUTLIER) cc_final: 0.6714 (p90) REVERT: D 530 MET cc_start: 0.6937 (mtp) cc_final: 0.6601 (ttt) REVERT: D 655 LYS cc_start: 0.8706 (tptp) cc_final: 0.8122 (pttt) REVERT: G 166 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8062 (mtp85) REVERT: G 173 TYR cc_start: 0.8659 (m-80) cc_final: 0.8453 (m-80) REVERT: H 33 GLU cc_start: 0.7881 (tt0) cc_final: 0.7614 (tt0) REVERT: L 82 ASP cc_start: 0.7830 (m-30) cc_final: 0.6764 (t0) REVERT: E 62 ASP cc_start: 0.8358 (t0) cc_final: 0.7852 (t0) REVERT: E 74 ASP cc_start: 0.7856 (m-30) cc_final: 0.7630 (m-30) REVERT: F 62 ASP cc_start: 0.8343 (t0) cc_final: 0.8076 (t0) REVERT: K 37 GLN cc_start: 0.8340 (tt0) cc_final: 0.7985 (tt0) outliers start: 41 outliers final: 28 residues processed: 374 average time/residue: 0.3414 time to fit residues: 190.0924 Evaluate side-chains 359 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 330 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain I residue 530 MET Chi-restraints excluded: chain I residue 611 ASN Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain J residue 78 MET Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 96 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 0.0020 chunk 123 optimal weight: 1.9990 chunk 219 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 363 GLN C 377 ASN G 377 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20025 Z= 0.245 Angle : 0.639 10.003 27165 Z= 0.316 Chirality : 0.047 0.239 3318 Planarity : 0.004 0.062 3309 Dihedral : 7.669 57.878 4488 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.54 % Favored : 94.19 % Rotamer: Outliers : 2.37 % Allowed : 13.91 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.29 (0.18), residues: 2256 helix: 1.74 (0.27), residues: 402 sheet: 0.06 (0.18), residues: 795 loop : -1.15 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 112 HIS 0.004 0.001 HIS A 374 PHE 0.017 0.001 PHE C 376 TYR 0.017 0.001 TYR G 191 ARG 0.008 0.000 ARG J 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 350 time to evaluate : 2.206 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7046 (mm-30) REVERT: A 191 TYR cc_start: 0.8771 (m-80) cc_final: 0.8522 (m-80) REVERT: B 535 MET cc_start: 0.7769 (mpp) cc_final: 0.7450 (mmm) REVERT: C 173 TYR cc_start: 0.8463 (m-80) cc_final: 0.8233 (m-80) REVERT: C 191 TYR cc_start: 0.8806 (m-80) cc_final: 0.8580 (m-80) REVERT: C 316 TRP cc_start: 0.7451 (OUTLIER) cc_final: 0.6818 (p90) REVERT: D 530 MET cc_start: 0.6900 (mtp) cc_final: 0.6634 (ttt) REVERT: D 655 LYS cc_start: 0.8662 (tptp) cc_final: 0.8234 (pttt) REVERT: G 166 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8106 (mtp85) REVERT: H 33 GLU cc_start: 0.7989 (tt0) cc_final: 0.7703 (tt0) REVERT: L 54 ARG cc_start: 0.8516 (ptp90) cc_final: 0.7941 (ptp90) REVERT: E 62 ASP cc_start: 0.8459 (t0) cc_final: 0.7999 (t0) REVERT: E 74 ASP cc_start: 0.7867 (m-30) cc_final: 0.7663 (m-30) REVERT: K 37 GLN cc_start: 0.8364 (tt0) cc_final: 0.8040 (tt0) outliers start: 48 outliers final: 37 residues processed: 373 average time/residue: 0.3558 time to fit residues: 197.0559 Evaluate side-chains 369 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 331 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain I residue 530 MET Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20025 Z= 0.234 Angle : 0.635 9.658 27165 Z= 0.315 Chirality : 0.047 0.237 3318 Planarity : 0.004 0.064 3309 Dihedral : 7.480 57.381 4488 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.50 % Favored : 94.24 % Rotamer: Outliers : 2.27 % Allowed : 14.25 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2256 helix: 1.74 (0.27), residues: 402 sheet: 0.07 (0.19), residues: 789 loop : -1.18 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 50 HIS 0.004 0.001 HIS A 374 PHE 0.017 0.001 PHE C 376 TYR 0.016 0.001 TYR G 191 ARG 0.009 0.001 ARG F 82A *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 344 time to evaluate : 2.008 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7051 (mm-30) REVERT: A 191 TYR cc_start: 0.8790 (m-80) cc_final: 0.8539 (m-80) REVERT: B 535 MET cc_start: 0.7703 (mpp) cc_final: 0.7420 (mmm) REVERT: C 112 TRP cc_start: 0.8367 (t-100) cc_final: 0.8115 (t-100) REVERT: C 173 TYR cc_start: 0.8458 (m-80) cc_final: 0.8229 (m-80) REVERT: C 191 TYR cc_start: 0.8796 (m-80) cc_final: 0.8580 (m-80) REVERT: D 530 MET cc_start: 0.6877 (mtp) cc_final: 0.6608 (ttt) REVERT: D 655 LYS cc_start: 0.8665 (tptp) cc_final: 0.8231 (pttt) REVERT: G 166 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8112 (mtp85) REVERT: G 363 GLN cc_start: 0.7851 (mt0) cc_final: 0.7641 (mm-40) REVERT: I 601 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7802 (ptmt) REVERT: H 33 GLU cc_start: 0.8026 (tt0) cc_final: 0.7750 (tt0) REVERT: L 54 ARG cc_start: 0.8535 (ptp90) cc_final: 0.7987 (ptp90) REVERT: L 82 ASP cc_start: 0.7869 (m-30) cc_final: 0.6813 (t0) REVERT: E 62 ASP cc_start: 0.8527 (t0) cc_final: 0.8074 (t0) REVERT: E 74 ASP cc_start: 0.7867 (m-30) cc_final: 0.7624 (m-30) REVERT: K 37 GLN cc_start: 0.8387 (tt0) cc_final: 0.8019 (tt0) outliers start: 46 outliers final: 41 residues processed: 367 average time/residue: 0.3553 time to fit residues: 192.7663 Evaluate side-chains 368 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 327 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 530 MET Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 96 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20025 Z= 0.308 Angle : 0.666 9.566 27165 Z= 0.333 Chirality : 0.048 0.241 3318 Planarity : 0.004 0.058 3309 Dihedral : 7.542 56.597 4488 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.34 % Favored : 93.40 % Rotamer: Outliers : 2.51 % Allowed : 14.05 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2256 helix: 1.43 (0.27), residues: 420 sheet: 0.03 (0.19), residues: 792 loop : -1.25 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 112 HIS 0.006 0.002 HIS A 374 PHE 0.019 0.002 PHE C 376 TYR 0.024 0.001 TYR D 638 ARG 0.008 0.001 ARG F 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 331 time to evaluate : 2.170 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6945 (mm-30) REVERT: A 191 TYR cc_start: 0.8803 (m-80) cc_final: 0.8543 (m-80) REVERT: B 535 MET cc_start: 0.7734 (mpp) cc_final: 0.7464 (mmm) REVERT: C 173 TYR cc_start: 0.8473 (m-80) cc_final: 0.8243 (m-80) REVERT: C 191 TYR cc_start: 0.8743 (m-80) cc_final: 0.8528 (m-80) REVERT: D 530 MET cc_start: 0.6957 (mtp) cc_final: 0.6739 (ttt) REVERT: D 655 LYS cc_start: 0.8683 (tptp) cc_final: 0.8212 (pttt) REVERT: G 166 ARG cc_start: 0.8557 (mtp85) cc_final: 0.8120 (mtp85) REVERT: I 601 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7711 (ptmt) REVERT: L 82 ASP cc_start: 0.7769 (m-30) cc_final: 0.6777 (t0) REVERT: E 62 ASP cc_start: 0.8640 (t0) cc_final: 0.8297 (t0) REVERT: K 37 GLN cc_start: 0.8392 (tt0) cc_final: 0.8030 (tt0) REVERT: K 82 ASP cc_start: 0.7624 (m-30) cc_final: 0.7209 (t0) outliers start: 51 outliers final: 46 residues processed: 357 average time/residue: 0.3947 time to fit residues: 210.7372 Evaluate side-chains 377 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 331 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain I residue 530 MET Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 96 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 150 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20025 Z= 0.257 Angle : 0.645 9.663 27165 Z= 0.321 Chirality : 0.047 0.238 3318 Planarity : 0.004 0.058 3309 Dihedral : 7.418 56.959 4488 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.67 % Favored : 94.10 % Rotamer: Outliers : 2.42 % Allowed : 14.15 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2256 helix: 1.65 (0.27), residues: 402 sheet: -0.01 (0.18), residues: 795 loop : -1.24 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 112 HIS 0.005 0.001 HIS A 374 PHE 0.018 0.001 PHE C 376 TYR 0.028 0.001 TYR D 638 ARG 0.007 0.001 ARG F 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 340 time to evaluate : 2.325 Fit side-chains revert: symmetry clash REVERT: A 88 ASN cc_start: 0.8528 (t0) cc_final: 0.8296 (t0) REVERT: A 91 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7033 (mm-30) REVERT: A 191 TYR cc_start: 0.8821 (m-80) cc_final: 0.8563 (m-80) REVERT: C 173 TYR cc_start: 0.8437 (m-80) cc_final: 0.8203 (m-80) REVERT: C 191 TYR cc_start: 0.8740 (m-80) cc_final: 0.8539 (m-80) REVERT: D 530 MET cc_start: 0.6905 (mtp) cc_final: 0.6685 (ttt) REVERT: D 655 LYS cc_start: 0.8682 (tptp) cc_final: 0.8212 (pttt) REVERT: G 166 ARG cc_start: 0.8488 (mtp85) cc_final: 0.8199 (mtp85) REVERT: I 601 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7728 (ptmt) REVERT: H 33 GLU cc_start: 0.8067 (tt0) cc_final: 0.7800 (tt0) REVERT: L 82 ASP cc_start: 0.7974 (m-30) cc_final: 0.6894 (t0) REVERT: E 62 ASP cc_start: 0.8645 (t0) cc_final: 0.8306 (t0) REVERT: E 74 ASP cc_start: 0.7862 (m-30) cc_final: 0.7603 (m-30) REVERT: K 37 GLN cc_start: 0.8375 (tt0) cc_final: 0.8002 (tt0) REVERT: K 82 ASP cc_start: 0.7508 (m-30) cc_final: 0.7237 (t0) outliers start: 49 outliers final: 46 residues processed: 366 average time/residue: 0.3514 time to fit residues: 191.7124 Evaluate side-chains 377 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 331 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 96 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113668 restraints weight = 32124.719| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.12 r_work: 0.3324 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20025 Z= 0.258 Angle : 0.649 9.569 27165 Z= 0.323 Chirality : 0.047 0.238 3318 Planarity : 0.004 0.056 3309 Dihedral : 7.369 56.969 4488 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.25 % Favored : 93.53 % Rotamer: Outliers : 2.32 % Allowed : 14.50 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.46 (0.18), residues: 2256 helix: 1.66 (0.27), residues: 402 sheet: -0.01 (0.18), residues: 795 loop : -1.31 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 614 HIS 0.005 0.001 HIS A 374 PHE 0.017 0.001 PHE C 376 TYR 0.052 0.002 TYR D 638 ARG 0.007 0.000 ARG F 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4522.60 seconds wall clock time: 83 minutes 26.77 seconds (5006.77 seconds total)