Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 22:57:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/05_2023/8sav_40281_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/05_2023/8sav_40281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/05_2023/8sav_40281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/05_2023/8sav_40281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/05_2023/8sav_40281_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/05_2023/8sav_40281_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 138 5.16 5 C 12771 2.51 5 N 3528 2.21 5 O 4014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G ASP 86": "OD1" <-> "OD2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 275": "OE1" <-> "OE2" Residue "I PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 589": "OD1" <-> "OD2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "L PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 20451 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "B" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "F" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "H" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "J" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" 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 chiralities: 5 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" 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 chiralities: 5 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.66, per 1000 atoms: 0.52 Number of scatterers: 20451 At special positions: 0 Unit cell: (142.844, 149.24, 121.524, 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 138 16.00 O 4014 8.00 N 3528 7.00 C 12771 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 5 " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A 601 " - " ASN A 138 " " NAG A 602 " - " ASN A 392 " " NAG E 601 " - " ASN E 138 " " NAG E 602 " - " ASN E 392 " " NAG I 601 " - " ASN I 138 " " NAG I 602 " - " ASN I 392 " " NAG M 1 " - " ASN A 386 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 396 " " NAG R 1 " - " ASN E 386 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 156 " " NAG U 1 " - " ASN E 262 " " NAG V 1 " - " ASN E 396 " " NAG W 1 " - " ASN I 386 " " NAG X 1 " - " ASN I 332 " " NAG Y 1 " - " ASN I 156 " " NAG Z 1 " - " ASN I 262 " " NAG a 1 " - " ASN I 396 " Time building additional restraints: 9.33 Conformation dependent library (CDL) restraints added in 3.0 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4638 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 42 sheets defined 20.1% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.500A pdb=" N THR A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.841A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 536 through 544 Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.882A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 4.106A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.506A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.974A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 461 through 464 removed outlier: 3.664A pdb=" N LYS E 463 " --> pdb=" O ASN E 461 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 464 " --> pdb=" O SER E 461l" (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 461 through 464' Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.508A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.833A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 4.333A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.512A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 4.026A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.725A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.616A pdb=" N PHE H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 353 removed outlier: 3.582A pdb=" N HIS I 352 " --> pdb=" O GLU I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 461 through 464 removed outlier: 3.532A pdb=" N LYS I 463 " --> pdb=" O ASN I 461 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR I 464 " --> pdb=" O SER I 461l" (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 461 through 464' Processing helix chain 'I' and resid 474 through 484 removed outlier: 3.542A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 544 Processing helix chain 'J' and resid 570 through 596 removed outlier: 3.889A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 625 removed outlier: 4.246A pdb=" N ASP J 624 " --> pdb=" O SER J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 removed outlier: 4.384A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 removed outlier: 3.735A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU J 647 " --> pdb=" O TYR J 643 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP J 664 " --> pdb=" O LEU J 660 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.666A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.510A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.442A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.619A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) 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 177 removed outlier: 3.807A pdb=" N ARG A 192 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.516A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 360 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.064A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 421 removed outlier: 3.849A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 309 removed outlier: 6.125A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.536A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET C 18 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 82 " --> pdb=" O MET C 18 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 68 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.695A pdb=" N GLN C 10 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 109 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP C 36 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN C 58 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.803A pdb=" N THR D 5 " --> pdb=" O ARG D 24 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.551A pdb=" N VAL D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN D 89 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 34 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.548A pdb=" N GLN D 90 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.313A pdb=" N TRP E 35 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.616A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.804A pdb=" N ARG E 192 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.623A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.598A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 360 through 361 Processing sheet with id=AC3, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.065A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.598A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 421 removed outlier: 3.815A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 301 through 309 removed outlier: 6.237A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 423 through 425 Processing sheet with id=AC6, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.754A pdb=" N MET G 18 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.625A pdb=" N GLN G 10 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN G 58 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 4 through 7 removed outlier: 4.216A pdb=" N ASP H 70 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AD1, first strand: chain 'H' and resid 53 through 54 removed outlier: 5.849A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 34 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN H 89 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 494 through 499 removed outlier: 3.570A pdb=" N THR I 499 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP I 35 " --> pdb=" O THR I 499 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.618A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD5, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AD6, first strand: chain 'I' and resid 169 through 177 removed outlier: 3.844A pdb=" N ARG I 192 " --> pdb=" O VAL I 182 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.271A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 259 through 261 removed outlier: 10.239A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.578A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N LYS I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL I 292 " --> pdb=" O LYS I 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 298 current: chain 'I' and resid 360 through 361 Processing sheet with id=AD9, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.039A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL I 292 " --> pdb=" O LYS I 446 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N LYS I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.578A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 443 through 456 current: chain 'I' and resid 413 through 421 removed outlier: 3.842A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 301 through 309 removed outlier: 6.070A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.560A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET K 18 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU K 82 " --> pdb=" O MET K 18 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.718A pdb=" N GLN K 10 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP K 36 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.283A pdb=" N ASP L 70 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.622A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.549A pdb=" N GLN L 90 " --> pdb=" O PHE L 97 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1788 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: 6.71 Time building geometry restraints manager: 9.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6597 1.34 - 1.46: 4987 1.46 - 1.58: 9086 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 20856 Sorted by residual: bond pdb=" C TRP C 100B" pdb=" N ASP C 100C" ideal model delta sigma weight residual 1.333 1.375 -0.042 1.38e-02 5.25e+03 9.44e+00 bond pdb=" C TRP K 100B" pdb=" N ASP K 100C" ideal model delta sigma weight residual 1.333 1.367 -0.034 1.38e-02 5.25e+03 6.12e+00 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 20851 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.87: 432 105.87 - 112.96: 11312 112.96 - 120.04: 7250 120.04 - 127.13: 9005 127.13 - 134.21: 297 Bond angle restraints: 28296 Sorted by residual: angle pdb=" C ASP G 100C" pdb=" N PHE G 100D" pdb=" CA PHE G 100D" ideal model delta sigma weight residual 121.70 134.17 -12.47 1.80e+00 3.09e-01 4.80e+01 angle pdb=" C ASP C 100C" pdb=" N PHE C 100D" pdb=" CA PHE C 100D" ideal model delta sigma weight residual 121.70 133.88 -12.18 1.80e+00 3.09e-01 4.58e+01 angle pdb=" C ASP K 100C" pdb=" N PHE K 100D" pdb=" CA PHE K 100D" ideal model delta sigma weight residual 121.70 133.20 -11.50 1.80e+00 3.09e-01 4.08e+01 angle pdb=" C THR A 460 " pdb=" N ASN A 461 " pdb=" CA ASN A 461 " ideal model delta sigma weight residual 121.70 132.14 -10.44 1.80e+00 3.09e-01 3.37e+01 angle pdb=" C THR E 460 " pdb=" N ASN E 461 " pdb=" CA ASN E 461 " ideal model delta sigma weight residual 121.70 131.99 -10.29 1.80e+00 3.09e-01 3.27e+01 ... (remaining 28291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 11124 17.88 - 35.77: 821 35.77 - 53.65: 155 53.65 - 71.53: 47 71.53 - 89.42: 27 Dihedral angle restraints: 12174 sinusoidal: 4950 harmonic: 7224 Sorted by residual: dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.62 -65.62 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.23 -65.23 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 157.99 -64.99 1 1.00e+01 1.00e-02 5.54e+01 ... (remaining 12171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2649 0.057 - 0.114: 491 0.114 - 0.172: 139 0.172 - 0.229: 8 0.229 - 0.286: 16 Chirality restraints: 3303 Sorted by residual: chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3300 not shown) Planarity restraints: 3591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 100D" -0.030 2.00e-02 2.50e+03 2.91e-02 1.48e+01 pdb=" CG PHE G 100D" 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE G 100D" -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE G 100D" -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE G 100D" 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 100D" -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE G 100D" -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 50 " 0.018 2.00e-02 2.50e+03 1.89e-02 8.89e+00 pdb=" CG TRP K 50 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP K 50 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP K 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP K 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 50 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 50 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 50 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP K 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 58 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO D 59 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " -0.035 5.00e-02 4.00e+02 ... (remaining 3588 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 160 2.58 - 3.16: 17230 3.16 - 3.74: 29491 3.74 - 4.32: 41034 4.32 - 4.90: 69523 Nonbonded interactions: 157438 Sorted by model distance: nonbonded pdb=" O ASP G 100C" pdb=" OH TYR H 36 " model vdw 2.003 2.440 nonbonded pdb=" O ASP K 100C" pdb=" OH TYR L 36 " model vdw 2.042 2.440 nonbonded pdb=" O ASP C 100C" pdb=" OH TYR D 36 " model vdw 2.044 2.440 nonbonded pdb=" O ASN A 461 " pdb=" OG1 THR A 464 " model vdw 2.108 2.440 nonbonded pdb=" OD1 ASN A 461 " pdb=" OG1 THR A 464 " model vdw 2.192 2.440 ... (remaining 157433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 8.740 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 53.200 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.260 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.005 0.047 20856 Z= 0.332 Angle : 0.918 12.470 28296 Z= 0.491 Chirality : 0.053 0.286 3303 Planarity : 0.005 0.064 3570 Dihedral : 13.888 89.416 7410 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.58 % Favored : 93.18 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.54 (0.16), residues: 2478 helix: 0.26 (0.25), residues: 411 sheet: -0.74 (0.18), residues: 759 loop : -1.63 (0.17), residues: 1308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 2.605 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 200 average time/residue: 0.2951 time to fit residues: 96.8251 Evaluate side-chains 132 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 145 optimal weight: 0.0070 chunk 226 optimal weight: 4.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 105 HIS ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS F 540 GLN F 658 GLN G 102 HIS J 540 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 20856 Z= 0.389 Angle : 0.831 14.792 28296 Z= 0.434 Chirality : 0.052 0.418 3303 Planarity : 0.005 0.047 3570 Dihedral : 6.934 82.675 2739 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.07 % Favored : 91.69 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.71 (0.16), residues: 2478 helix: 0.28 (0.26), residues: 393 sheet: -0.65 (0.19), residues: 723 loop : -1.88 (0.16), residues: 1362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 155 average time/residue: 0.2869 time to fit residues: 74.3654 Evaluate side-chains 139 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 2.501 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1993 time to fit residues: 10.0015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 20856 Z= 0.184 Angle : 0.693 13.609 28296 Z= 0.361 Chirality : 0.046 0.412 3303 Planarity : 0.004 0.043 3570 Dihedral : 6.472 78.860 2739 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.61 % Favored : 94.15 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.44 (0.16), residues: 2478 helix: 0.58 (0.26), residues: 393 sheet: -0.44 (0.19), residues: 690 loop : -1.74 (0.16), residues: 1395 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 161 average time/residue: 0.3046 time to fit residues: 82.5201 Evaluate side-chains 136 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 2.628 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2082 time to fit residues: 6.7563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN A 461 ASN B 611 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN I 428 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 20856 Z= 0.398 Angle : 0.793 14.394 28296 Z= 0.413 Chirality : 0.050 0.365 3303 Planarity : 0.005 0.046 3570 Dihedral : 6.670 77.256 2739 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.39 % Favored : 91.32 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.71 (0.16), residues: 2478 helix: 0.17 (0.25), residues: 411 sheet: -0.47 (0.19), residues: 726 loop : -1.99 (0.16), residues: 1341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 2.521 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 162 average time/residue: 0.2854 time to fit residues: 78.2411 Evaluate side-chains 142 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 2.574 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2034 time to fit residues: 12.6574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN E 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 20856 Z= 0.227 Angle : 0.695 13.420 28296 Z= 0.362 Chirality : 0.046 0.368 3303 Planarity : 0.004 0.055 3570 Dihedral : 6.444 76.682 2739 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.05 % Favored : 93.70 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % 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: -1.55 (0.16), residues: 2478 helix: 0.49 (0.25), residues: 411 sheet: -0.49 (0.19), residues: 687 loop : -1.85 (0.16), residues: 1380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 2.419 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 148 average time/residue: 0.2901 time to fit residues: 72.7985 Evaluate side-chains 131 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1913 time to fit residues: 7.6602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 0.0050 chunk 59 optimal weight: 6.9990 chunk 240 optimal weight: 0.3980 chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 20856 Z= 0.192 Angle : 0.665 12.781 28296 Z= 0.345 Chirality : 0.045 0.331 3303 Planarity : 0.004 0.042 3570 Dihedral : 6.206 80.206 2739 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.97 % Favored : 93.79 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % 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: -1.41 (0.16), residues: 2478 helix: 0.64 (0.26), residues: 411 sheet: -0.39 (0.19), residues: 672 loop : -1.75 (0.16), residues: 1395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 2.491 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 143 average time/residue: 0.3043 time to fit residues: 74.2000 Evaluate side-chains 128 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 2.564 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2492 time to fit residues: 6.7867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 137 optimal weight: 0.1980 chunk 175 optimal weight: 0.1980 chunk 136 optimal weight: 0.9980 chunk 202 optimal weight: 0.5980 chunk 134 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 461 ASN B 611 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS I 287 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 20856 Z= 0.159 Angle : 0.655 12.557 28296 Z= 0.337 Chirality : 0.045 0.311 3303 Planarity : 0.004 0.050 3570 Dihedral : 6.032 83.891 2739 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.93 % Favored : 93.83 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % 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: -1.20 (0.17), residues: 2478 helix: 0.82 (0.26), residues: 411 sheet: -0.27 (0.19), residues: 684 loop : -1.62 (0.16), residues: 1383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 2.694 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 137 average time/residue: 0.2937 time to fit residues: 68.1925 Evaluate side-chains 125 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 2.375 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1907 time to fit residues: 4.5802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 chunk 143 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 20856 Z= 0.332 Angle : 0.746 13.296 28296 Z= 0.387 Chirality : 0.048 0.333 3303 Planarity : 0.005 0.050 3570 Dihedral : 6.327 82.555 2739 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.51 % Favored : 91.24 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % 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: -1.52 (0.16), residues: 2478 helix: 0.56 (0.26), residues: 411 sheet: -0.48 (0.20), residues: 687 loop : -1.83 (0.16), residues: 1380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 2.500 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 0.3158 time to fit residues: 71.4152 Evaluate side-chains 126 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 2.522 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2213 time to fit residues: 7.2685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 20856 Z= 0.236 Angle : 0.701 12.592 28296 Z= 0.362 Chirality : 0.046 0.330 3303 Planarity : 0.004 0.040 3570 Dihedral : 6.242 82.920 2739 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.86 % Favored : 92.90 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % 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: -1.43 (0.16), residues: 2478 helix: 0.68 (0.26), residues: 411 sheet: -0.41 (0.19), residues: 696 loop : -1.82 (0.16), residues: 1371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 2.631 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 135 average time/residue: 0.3026 time to fit residues: 68.8653 Evaluate side-chains 128 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 2.792 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2227 time to fit residues: 6.1761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 20856 Z= 0.289 Angle : 0.729 13.129 28296 Z= 0.376 Chirality : 0.047 0.335 3303 Planarity : 0.004 0.045 3570 Dihedral : 6.315 83.438 2739 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.39 % Favored : 91.36 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % 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: -1.53 (0.16), residues: 2478 helix: 0.60 (0.26), residues: 411 sheet: -0.52 (0.20), residues: 687 loop : -1.84 (0.16), residues: 1380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 2.516 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 125 average time/residue: 0.2966 time to fit residues: 62.7254 Evaluate side-chains 123 residues out of total 2181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 2.737 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2250 time to fit residues: 5.1970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 182 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 0.1980 chunk 197 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 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 = 0.3748 r_free = 0.3748 target = 0.089651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077348 restraints weight = 69240.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077976 restraints weight = 56433.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.078704 restraints weight = 45304.276| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 20856 Z= 0.218 Angle : 0.697 12.699 28296 Z= 0.360 Chirality : 0.046 0.328 3303 Planarity : 0.004 0.042 3570 Dihedral : 6.236 84.631 2739 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.74 % Favored : 93.06 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % 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: -1.40 (0.16), residues: 2478 helix: 0.73 (0.26), residues: 411 sheet: -0.42 (0.20), residues: 681 loop : -1.77 (0.16), residues: 1386 =============================================================================== Job complete usr+sys time: 2834.85 seconds wall clock time: 54 minutes 5.04 seconds (3245.04 seconds total)