Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 02:05:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mep_23801/04_2023/7mep_23801.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mep_23801/04_2023/7mep_23801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mep_23801/04_2023/7mep_23801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mep_23801/04_2023/7mep_23801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mep_23801/04_2023/7mep_23801.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mep_23801/04_2023/7mep_23801.pdb" } resolution = 3.5 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= 0.002 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 128 5.16 5 C 13518 2.51 5 N 3635 2.21 5 O 4355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "N PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 381": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 21636 Number of models: 1 Model: "" Number of chains: 35 Chain: "G" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3477 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 985 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 995 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3487 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 985 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "N" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "D" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3499 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 20, 'TRANS': 422} Chain breaks: 3 Chain: "F" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 985 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "O" 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: "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 chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.17, per 1000 atoms: 0.56 Number of scatterers: 21636 At special positions: 0 Unit cell: (130.81, 126.69, 172.01, 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 128 16.00 O 4355 8.00 N 3635 7.00 C 13518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 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=2.03 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=2.02 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 H 22 " - pdb=" SG CYS H 92 " 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=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 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=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.06 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.07 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 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 O 3 " - " MAN O 4 " " BMA U 3 " - " MAN U 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA U 3 " - " MAN U 5 " " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 276 " " NAG A 703 " - " ASN A 386 " " NAG A 704 " - " ASN A 363 " " NAG A 705 " - " ASN A 234 " " NAG A 706 " - " ASN A 197 " " NAG A 707 " - " ASN A 133 " " NAG A 708 " - " ASN A 88 " " NAG A 709 " - " ASN A 241 " " NAG A 710 " - " ASN A 289 " " NAG A 711 " - " ASN A 339 " " NAG A 712 " - " ASN A 355 " " NAG A 713 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 448 " " NAG C 702 " - " ASN C 160 " " NAG C 703 " - " ASN C 276 " " NAG C 704 " - " ASN C 386 " " NAG C 705 " - " ASN C 363 " " NAG C 706 " - " ASN C 234 " " NAG C 707 " - " ASN C 197 " " NAG C 708 " - " ASN C 133 " " NAG C 709 " - " ASN C 301 " " NAG C 710 " - " ASN C 88 " " NAG C 711 " - " ASN C 241 " " NAG C 712 " - " ASN C 289 " " NAG C 713 " - " ASN C 339 " " NAG C 714 " - " ASN C 355 " " NAG C 715 " - " ASN C 392 " " NAG D 701 " - " ASN D 160 " " NAG D 702 " - " ASN D 276 " " NAG D 703 " - " ASN D 295 " " NAG D 704 " - " ASN D 386 " " NAG D 705 " - " ASN D 363 " " NAG D 706 " - " ASN D 234 " " NAG D 707 " - " ASN D 197 " " NAG D 708 " - " ASN D 133 " " NAG D 709 " - " ASN D 88 " " NAG D 710 " - " ASN D 241 " " NAG D 711 " - " ASN D 289 " " NAG D 712 " - " ASN D 339 " " NAG D 713 " - " ASN D 355 " " NAG D 714 " - " ASN D 392 " " NAG E 701 " - " ASN E 637 " " NAG E 702 " - " ASN E 618 " " NAG E 703 " - " ASN E 611 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 448 " " NAG Q 1 " - " ASN A 295 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 295 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN D 262 " " NAG Z 1 " - " ASN D 448 " " NAG a 1 " - " ASN D 156 " " NAG b 1 " - " ASN D 301 " " NAG c 1 " - " ASN D 332 " Time building additional restraints: 9.73 Conformation dependent library (CDL) restraints added in 3.2 seconds 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 49 sheets defined 21.3% alpha, 45.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 60 through 65 removed outlier: 4.448A pdb=" N SER I 65 " --> pdb=" O PRO I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.099A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.833A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.600A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.416A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 535 through 541 removed outlier: 5.869A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 539 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.838A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 657 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.931A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.084A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 65 removed outlier: 5.403A pdb=" N SER M 65 " --> pdb=" O SER M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.156A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.889A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.976A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.407A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.524A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.769A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 657 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.728A pdb=" N VAL K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 removed outlier: 5.320A pdb=" N SER N 65 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.518A pdb=" N THR N 87 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.122A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 354 removed outlier: 4.005A pdb=" N VAL D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 535 through 541 removed outlier: 5.813A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL F 539 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.747A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.491A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AA4, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.828A pdb=" N GLY I 44 " --> pdb=" O THR I 40 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP I 35 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.828A pdb=" N GLY I 44 " --> pdb=" O THR I 40 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP I 35 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.396A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB2, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.515A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.413A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.125A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.841A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.517A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.590A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.590A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.623A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'M' and resid 57 through 59 removed outlier: 4.845A pdb=" N GLY M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR M 50 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 57 through 59 removed outlier: 4.845A pdb=" N GLY M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR M 50 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.916A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.332A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD4, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.569A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.276A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.956A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.523A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AD9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.903A pdb=" N ALA K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.903A pdb=" N ALA K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'N' and resid 57 through 59 removed outlier: 4.068A pdb=" N GLY N 44 " --> pdb=" O THR N 40 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR N 50 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP N 35 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 57 through 59 removed outlier: 4.068A pdb=" N GLY N 44 " --> pdb=" O THR N 40 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR N 50 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP N 35 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.345A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AE7, first strand: chain 'D' and resid 75 through 76 removed outlier: 4.074A pdb=" N VAL D 75 " --> pdb=" O CYS D 54 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE9, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AF1, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.523A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 394 through 395 removed outlier: 6.259A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.667A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.997A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.667A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.659A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) 917 hydrogen bonds defined for protein. 2370 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: 8.79 Time building geometry restraints manager: 10.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5042 1.32 - 1.46: 6975 1.46 - 1.59: 9820 1.59 - 1.73: 86 1.73 - 1.87: 157 Bond restraints: 22080 Sorted by residual: bond pdb=" NE ARG C 504 " pdb=" CZ ARG C 504 " ideal model delta sigma weight residual 1.326 1.414 -0.088 1.10e-02 8.26e+03 6.37e+01 bond pdb=" NE ARG K 3 " pdb=" CZ ARG K 3 " ideal model delta sigma weight residual 1.326 1.405 -0.079 1.10e-02 8.26e+03 5.11e+01 bond pdb=" CG GLN K 6 " pdb=" CD GLN K 6 " ideal model delta sigma weight residual 1.516 1.353 0.163 2.50e-02 1.60e+03 4.23e+01 bond pdb=" NE ARG J 3 " pdb=" CZ ARG J 3 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.07e+01 bond pdb=" NE1 TRP I 96 " pdb=" CE2 TRP I 96 " ideal model delta sigma weight residual 1.370 1.303 0.067 1.10e-02 8.26e+03 3.71e+01 ... (remaining 22075 not shown) Histogram of bond angle deviations from ideal: 95.10 - 103.20: 246 103.20 - 111.31: 9313 111.31 - 119.41: 9788 119.41 - 127.51: 10371 127.51 - 135.62: 284 Bond angle restraints: 30002 Sorted by residual: angle pdb=" N ASP B 659 " pdb=" CA ASP B 659 " pdb=" C ASP B 659 " ideal model delta sigma weight residual 111.28 120.99 -9.71 1.09e+00 8.42e-01 7.94e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 128.55 -8.99 1.02e+00 9.61e-01 7.76e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.02e+00 9.61e-01 7.74e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.01e+00 9.80e-01 6.88e+01 angle pdb=" C GLU D 492 " pdb=" N PRO D 493 " pdb=" CA PRO D 493 " ideal model delta sigma weight residual 119.56 127.96 -8.40 1.02e+00 9.61e-01 6.78e+01 ... (remaining 29997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 11980 17.56 - 35.12: 324 35.12 - 52.68: 100 52.68 - 70.24: 41 70.24 - 87.80: 20 Dihedral angle restraints: 12465 sinusoidal: 5002 harmonic: 7463 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.59 -66.59 1 1.00e+01 1.00e-02 5.79e+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 93.00 159.48 -66.48 1 1.00e+01 1.00e-02 5.77e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.78 -61.78 1 1.00e+01 1.00e-02 5.06e+01 ... (remaining 12462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2470 0.111 - 0.222: 758 0.222 - 0.333: 236 0.333 - 0.444: 127 0.444 - 0.555: 24 Chirality restraints: 3615 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.20e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 ... (remaining 3612 not shown) Planarity restraints: 3772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 706 " -0.226 2.00e-02 2.50e+03 1.89e-01 4.45e+02 pdb=" C7 NAG D 706 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG D 706 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG D 706 " 0.312 2.00e-02 2.50e+03 pdb=" O7 NAG D 706 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.172 2.00e-02 2.50e+03 1.42e-01 2.53e+02 pdb=" C7 NAG S 2 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.230 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 706 " 0.164 2.00e-02 2.50e+03 1.39e-01 2.40e+02 pdb=" C7 NAG C 706 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG C 706 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG C 706 " -0.224 2.00e-02 2.50e+03 pdb=" O7 NAG C 706 " 0.130 2.00e-02 2.50e+03 ... (remaining 3769 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5522 2.81 - 3.34: 19305 3.34 - 3.86: 35748 3.86 - 4.38: 42425 4.38 - 4.90: 69566 Nonbonded interactions: 172566 Sorted by model distance: nonbonded pdb=" O3 NAG E 702 " pdb=" O7 NAG E 702 " model vdw 2.293 2.440 nonbonded pdb=" N GLY L 50 " pdb=" O GLY L 50 " model vdw 2.370 2.496 nonbonded pdb=" O3 NAG S 2 " pdb=" O7 NAG S 2 " model vdw 2.385 2.440 nonbonded pdb=" NZ LYS A 207 " pdb=" OD2 ASP H 100C" model vdw 2.411 2.520 nonbonded pdb=" N ILE D 213 " pdb=" O ILE D 213 " model vdw 2.420 2.496 ... (remaining 172561 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' and (resid 33 through 504 or resid 701 through 713)) selection = (chain 'C' and (resid 33 through 57 or resid 66 through 185 or resid 189 through \ 504 or resid 702 through 714)) selection = (chain 'D' and (resid 33 through 57 or resid 66 through 185 or resid 189 through \ 504 or resid 701 through 713)) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 3 through 106) selection = chain 'J' selection = (chain 'K' and resid 3 through 106) } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.100 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 59.190 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.024 0.163 22080 Z= 1.522 Angle : 1.741 13.201 30002 Z= 1.143 Chirality : 0.138 0.555 3615 Planarity : 0.010 0.189 3706 Dihedral : 10.440 87.795 7536 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2544 helix: -0.29 (0.22), residues: 447 sheet: 0.92 (0.17), residues: 749 loop : 0.73 (0.17), residues: 1348 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 585 average time/residue: 0.4041 time to fit residues: 341.6616 Evaluate side-chains 299 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN H 105 GLN L 3 GLN L 32 GLN L 79 GLN J 42 GLN C 137 ASN C 300 ASN C 352 HIS E 658 GLN K 38 GLN K 89 HIS N 33 ASN D 66 HIS D 185 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 22080 Z= 0.258 Angle : 0.703 11.703 30002 Z= 0.366 Chirality : 0.049 0.311 3615 Planarity : 0.004 0.041 3706 Dihedral : 5.069 21.592 2780 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2544 helix: 1.46 (0.27), residues: 415 sheet: 0.94 (0.17), residues: 774 loop : 0.38 (0.17), residues: 1355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 378 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 29 residues processed: 403 average time/residue: 0.3698 time to fit residues: 224.6228 Evaluate side-chains 327 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 298 time to evaluate : 2.585 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 3 residues processed: 29 average time/residue: 0.2101 time to fit residues: 14.5875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 228 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN J 6 GLN C 137 ASN C 280 ASN K 38 GLN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22080 Z= 0.211 Angle : 0.591 10.068 30002 Z= 0.308 Chirality : 0.047 0.423 3615 Planarity : 0.004 0.043 3706 Dihedral : 4.746 20.011 2780 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.16), residues: 2544 helix: 1.67 (0.27), residues: 415 sheet: 0.93 (0.18), residues: 770 loop : 0.16 (0.17), residues: 1359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 342 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 358 average time/residue: 0.3794 time to fit residues: 202.6322 Evaluate side-chains 300 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 281 time to evaluate : 2.556 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.2031 time to fit residues: 10.6596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 25 optimal weight: 0.0060 chunk 109 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS L 3 GLN K 38 GLN K 92 ASN D 130 GLN D 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 22080 Z= 0.280 Angle : 0.599 10.695 30002 Z= 0.307 Chirality : 0.047 0.328 3615 Planarity : 0.004 0.054 3706 Dihedral : 4.720 19.725 2780 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2544 helix: 1.65 (0.27), residues: 414 sheet: 0.87 (0.18), residues: 787 loop : -0.00 (0.17), residues: 1343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 296 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 318 average time/residue: 0.3824 time to fit residues: 181.6425 Evaluate side-chains 301 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 278 time to evaluate : 2.737 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 0.2010 time to fit residues: 12.3531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 42 GLN ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN L 3 GLN J 6 GLN C 85 HIS K 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 22080 Z= 0.444 Angle : 0.682 11.178 30002 Z= 0.346 Chirality : 0.050 0.355 3615 Planarity : 0.005 0.050 3706 Dihedral : 5.033 21.116 2780 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2544 helix: 1.32 (0.27), residues: 414 sheet: 0.63 (0.18), residues: 798 loop : -0.29 (0.17), residues: 1332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 290 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 315 average time/residue: 0.4052 time to fit residues: 189.2768 Evaluate side-chains 295 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 274 time to evaluate : 2.684 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 2 residues processed: 21 average time/residue: 0.2008 time to fit residues: 11.2689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN L 3 GLN J 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 22080 Z= 0.163 Angle : 0.560 10.653 30002 Z= 0.285 Chirality : 0.045 0.295 3615 Planarity : 0.004 0.045 3706 Dihedral : 4.647 20.049 2780 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2544 helix: 1.72 (0.27), residues: 414 sheet: 0.68 (0.18), residues: 798 loop : -0.28 (0.17), residues: 1332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 321 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 330 average time/residue: 0.4022 time to fit residues: 195.6778 Evaluate side-chains 297 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 289 time to evaluate : 2.726 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2013 time to fit residues: 6.6072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 178 optimal weight: 0.0570 chunk 138 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN J 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 22080 Z= 0.318 Angle : 0.613 10.773 30002 Z= 0.310 Chirality : 0.047 0.326 3615 Planarity : 0.004 0.044 3706 Dihedral : 4.740 20.862 2780 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2544 helix: 1.67 (0.27), residues: 408 sheet: 0.55 (0.18), residues: 809 loop : -0.37 (0.17), residues: 1327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 285 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 296 average time/residue: 0.3915 time to fit residues: 171.7962 Evaluate side-chains 287 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 275 time to evaluate : 2.715 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.1954 time to fit residues: 7.9795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 145 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 77 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN J 6 GLN C 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 22080 Z= 0.185 Angle : 0.560 9.846 30002 Z= 0.285 Chirality : 0.045 0.290 3615 Planarity : 0.004 0.043 3706 Dihedral : 4.529 19.382 2780 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2544 helix: 1.86 (0.27), residues: 408 sheet: 0.63 (0.18), residues: 798 loop : -0.32 (0.17), residues: 1338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 298 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 305 average time/residue: 0.3854 time to fit residues: 175.1838 Evaluate side-chains 285 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 278 time to evaluate : 2.438 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.1897 time to fit residues: 5.7507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 0.0470 chunk 213 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 178 optimal weight: 0.0000 chunk 69 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN K 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 22080 Z= 0.157 Angle : 0.539 7.668 30002 Z= 0.276 Chirality : 0.045 0.280 3615 Planarity : 0.004 0.046 3706 Dihedral : 4.350 17.942 2780 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2544 helix: 1.88 (0.27), residues: 417 sheet: 0.64 (0.18), residues: 824 loop : -0.24 (0.17), residues: 1303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 302 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 307 average time/residue: 0.3940 time to fit residues: 180.9212 Evaluate side-chains 289 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 282 time to evaluate : 2.486 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.2036 time to fit residues: 6.3065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 231 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 30 ASN K 38 GLN F 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 22080 Z= 0.247 Angle : 0.572 7.409 30002 Z= 0.292 Chirality : 0.046 0.294 3615 Planarity : 0.004 0.044 3706 Dihedral : 4.463 18.693 2780 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2544 helix: 1.79 (0.27), residues: 417 sheet: 0.61 (0.18), residues: 812 loop : -0.33 (0.17), residues: 1315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 285 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 293 average time/residue: 0.3902 time to fit residues: 170.5742 Evaluate side-chains 279 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 271 time to evaluate : 2.704 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2030 time to fit residues: 6.6083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 84 optimal weight: 0.0670 chunk 206 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 176 optimal weight: 9.9990 overall best weight: 1.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 30 ASN J 6 GLN K 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096941 restraints weight = 37275.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099565 restraints weight = 21352.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101215 restraints weight = 14924.260| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 22080 Z= 0.178 Angle : 0.556 17.280 30002 Z= 0.281 Chirality : 0.045 0.279 3615 Planarity : 0.004 0.043 3706 Dihedral : 4.366 18.102 2780 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2544 helix: 1.89 (0.27), residues: 417 sheet: 0.61 (0.18), residues: 795 loop : -0.28 (0.17), residues: 1332 =============================================================================== Job complete usr+sys time: 4461.57 seconds wall clock time: 82 minutes 14.89 seconds (4934.89 seconds total)