Starting phenix.real_space_refine on Tue Mar 19 19:30:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y75_33652/03_2024/7y75_33652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y75_33652/03_2024/7y75_33652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y75_33652/03_2024/7y75_33652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y75_33652/03_2024/7y75_33652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y75_33652/03_2024/7y75_33652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y75_33652/03_2024/7y75_33652_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 S 146 5.16 5 C 16350 2.51 5 N 4004 2.21 5 O 4678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "E GLU 340": "OE1" <-> "OE2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D GLU 350": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D GLU 451": "OE1" <-> "OE2" Residue "D PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 430": "OE1" <-> "OE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ARG 518": "NH1" <-> "NH2" Residue "C GLU 564": "OE1" <-> "OE2" Residue "C GLU 571": "OE1" <-> "OE2" Residue "C GLU 639": "OE1" <-> "OE2" Residue "C ARG 671": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "C PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "F GLU 340": "OE1" <-> "OE2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F GLU 465": "OE1" <-> "OE2" Residue "F GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25186 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4499 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 552} Chain: "A" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6102 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain: "E" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4499 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 552} Chain: "C" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6102 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain: "F" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PH': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PH': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.73, per 1000 atoms: 0.51 Number of scatterers: 25186 At special positions: 0 Unit cell: (116.309, 151.093, 217.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 146 16.00 P 6 15.00 O 4678 8.00 N 4004 7.00 C 16350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.00 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.05 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.04 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG 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 V 1 " - " NAG V 2 " NAG-ASN " NAG A 901 " - " ASN A 322 " " NAG B1001 " - " ASN B 131 " " NAG B1002 " - " ASN B 332 " " NAG C 901 " - " ASN C 322 " " NAG D1001 " - " ASN D 131 " " NAG D1002 " - " ASN D 332 " " NAG G 1 " - " ASN B 357 " " NAG H 1 " - " ASN A 53 " " NAG I 1 " - " ASN A 90 " " NAG J 1 " - " ASN A 103 " " NAG K 1 " - " ASN A 432 " " NAG L 1 " - " ASN A 546 " " NAG M 1 " - " ASN A 690 " " NAG N 1 " - " ASN E 343 " " NAG O 1 " - " ASN D 357 " " NAG P 1 " - " ASN C 53 " " NAG Q 1 " - " ASN C 90 " " NAG R 1 " - " ASN C 103 " " NAG S 1 " - " ASN C 432 " " NAG T 1 " - " ASN C 546 " " NAG U 1 " - " ASN C 690 " " NAG V 1 " - " ASN F 343 " Time building additional restraints: 10.51 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 378 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 374 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 378 " 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 134 helices and 8 sheets defined 54.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 Processing helix chain 'B' and resid 30 through 37 Processing helix chain 'B' and resid 41 through 54 removed outlier: 4.244A pdb=" N VAL B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 57 through 69 Processing helix chain 'B' and resid 73 through 80 removed outlier: 4.357A pdb=" N TRP B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 86 through 116 removed outlier: 3.518A pdb=" N SER B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET B 100 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 141 No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.741A pdb=" N PHE B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 186 Processing helix chain 'B' and resid 196 through 216 removed outlier: 3.914A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Proline residue: B 203 - end of helix removed outlier: 3.857A pdb=" N THR B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.569A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 252 removed outlier: 3.960A pdb=" N ASN B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 272 through 320 removed outlier: 3.812A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 removed outlier: 4.213A pdb=" N ALA B 341 " --> pdb=" O LYS B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 354 removed outlier: 4.456A pdb=" N GLU B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Proline residue: B 353 - end of helix Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 388 through 415 removed outlier: 3.982A pdb=" N ALA B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 449 removed outlier: 3.767A pdb=" N MET B 446 " --> pdb=" O CYS B 442 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N PHE B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 482 removed outlier: 3.602A pdb=" N ASP B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 497 Processing helix chain 'B' and resid 503 through 510 removed outlier: 3.516A pdb=" N ALA B 510 " --> pdb=" O LYS B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 529 removed outlier: 4.028A pdb=" N VAL B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 567 removed outlier: 3.850A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 558 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 579 removed outlier: 3.767A pdb=" N PHE B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 52 Processing helix chain 'A' and resid 57 through 82 removed outlier: 3.760A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N MET A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 110 through 129 Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.880A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.590A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.691A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 removed outlier: 4.581A pdb=" N ASP A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.544A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.721A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.806A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 298 No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.695A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 367 through 384 removed outlier: 3.929A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 400 through 413 removed outlier: 4.023A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 432 through 446 removed outlier: 4.007A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 465 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 504 through 507 No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 513 through 532 removed outlier: 4.207A pdb=" N THR A 517 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN A 522 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS A 530 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN A 531 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 532 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.996A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 removed outlier: 3.894A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'A' and resid 624 through 628 Processing helix chain 'A' and resid 637 through 657 Processing helix chain 'A' and resid 667 through 669 No H-bonds generated for 'chain 'A' and resid 667 through 669' Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.638A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 766 removed outlier: 3.946A pdb=" N VAL A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 341 No H-bonds generated for 'chain 'E' and resid 338 through 341' Processing helix chain 'E' and resid 404 through 409 removed outlier: 4.713A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 421 removed outlier: 3.579A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 417 through 421' Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'D' and resid 12 through 22 Processing helix chain 'D' and resid 30 through 37 Processing helix chain 'D' and resid 41 through 54 removed outlier: 4.244A pdb=" N VAL D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 57 through 69 Processing helix chain 'D' and resid 73 through 80 removed outlier: 4.356A pdb=" N TRP D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 86 through 116 removed outlier: 3.518A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 141 No H-bonds generated for 'chain 'D' and resid 138 through 141' Processing helix chain 'D' and resid 144 through 150 removed outlier: 3.741A pdb=" N PHE D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 186 Processing helix chain 'D' and resid 196 through 216 removed outlier: 3.914A pdb=" N SER D 201 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Proline residue: D 203 - end of helix removed outlier: 3.857A pdb=" N THR D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 228 removed outlier: 3.569A pdb=" N LEU D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 252 removed outlier: 3.961A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 272 through 320 removed outlier: 3.812A pdb=" N ILE D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 341 removed outlier: 4.213A pdb=" N ALA D 341 " --> pdb=" O LYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 354 removed outlier: 4.457A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Proline residue: D 353 - end of helix Processing helix chain 'D' and resid 360 through 365 Processing helix chain 'D' and resid 373 through 378 Processing helix chain 'D' and resid 388 through 415 removed outlier: 3.983A pdb=" N ALA D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 449 removed outlier: 3.767A pdb=" N MET D 446 " --> pdb=" O CYS D 442 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL D 447 " --> pdb=" O ALA D 443 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N PHE D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR D 449 " --> pdb=" O GLY D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 482 removed outlier: 3.602A pdb=" N ASP D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 497 Processing helix chain 'D' and resid 503 through 510 removed outlier: 3.517A pdb=" N ALA D 510 " --> pdb=" O LYS D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 529 removed outlier: 4.028A pdb=" N VAL D 518 " --> pdb=" O PRO D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 567 removed outlier: 3.849A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL D 558 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 579 removed outlier: 3.766A pdb=" N PHE D 578 " --> pdb=" O ALA D 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 52 Processing helix chain 'C' and resid 57 through 82 removed outlier: 3.759A pdb=" N ALA C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 110 through 129 Processing helix chain 'C' and resid 148 through 154 removed outlier: 3.881A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 removed outlier: 3.591A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 177 through 194 removed outlier: 3.691A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 206 removed outlier: 4.581A pdb=" N ASP C 206 " --> pdb=" O TYR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.545A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 251 removed outlier: 3.721A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.806A pdb=" N TYR C 279 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER C 280 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 298 No H-bonds generated for 'chain 'C' and resid 295 through 298' Processing helix chain 'C' and resid 304 through 318 removed outlier: 3.694A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 330 No H-bonds generated for 'chain 'C' and resid 327 through 330' Processing helix chain 'C' and resid 367 through 384 removed outlier: 3.929A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 392 No H-bonds generated for 'chain 'C' and resid 390 through 392' Processing helix chain 'C' and resid 400 through 413 removed outlier: 4.023A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 432 through 446 removed outlier: 4.006A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 465 Processing helix chain 'C' and resid 473 through 483 Processing helix chain 'C' and resid 500 through 502 No H-bonds generated for 'chain 'C' and resid 500 through 502' Processing helix chain 'C' and resid 504 through 507 No H-bonds generated for 'chain 'C' and resid 504 through 507' Processing helix chain 'C' and resid 513 through 532 removed outlier: 4.207A pdb=" N THR C 517 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN C 522 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS C 530 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 531 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 532 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 541 No H-bonds generated for 'chain 'C' and resid 539 through 541' Processing helix chain 'C' and resid 548 through 560 removed outlier: 3.996A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 574 removed outlier: 3.893A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 587 Processing helix chain 'C' and resid 589 through 598 Processing helix chain 'C' and resid 624 through 628 Processing helix chain 'C' and resid 637 through 657 Processing helix chain 'C' and resid 667 through 669 No H-bonds generated for 'chain 'C' and resid 667 through 669' Processing helix chain 'C' and resid 697 through 706 Processing helix chain 'C' and resid 708 through 715 removed outlier: 3.638A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 766 removed outlier: 3.655A pdb=" N ARG C 766 " --> pdb=" O THR C 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 341 No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 404 through 409 removed outlier: 4.713A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.579A pdb=" N TYR F 421 " --> pdb=" O ASN F 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 417 through 421' Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing sheet with id= A, first strand: chain 'A' and resid 722 through 725 removed outlier: 4.647A pdb=" N LYS A 619 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.215A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.845A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 452 through 454 Processing sheet with id= E, first strand: chain 'C' and resid 722 through 725 removed outlier: 4.647A pdb=" N LYS C 619 " --> pdb=" O LEU C 725 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.216A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.845A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 452 through 454 1059 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.44 Time building geometry restraints manager: 11.29 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: 7722 1.34 - 1.47: 6850 1.47 - 1.59: 11036 1.59 - 1.72: 6 1.72 - 1.84: 232 Bond restraints: 25846 Sorted by residual: bond pdb=" C31 3PH B1003 " pdb=" O31 3PH B1003 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C31 3PH D1003 " pdb=" O31 3PH D1003 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C31 3PH D1005 " pdb=" O31 3PH D1005 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C31 3PH B1005 " pdb=" O31 3PH B1005 " ideal model delta sigma weight residual 1.325 1.454 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C21 3PH D1003 " pdb=" O21 3PH D1003 " ideal model delta sigma weight residual 1.328 1.456 -0.128 2.00e-02 2.50e+03 4.10e+01 ... (remaining 25841 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.75: 785 106.75 - 114.18: 14873 114.18 - 121.60: 14080 121.60 - 129.03: 5106 129.03 - 136.46: 234 Bond angle restraints: 35078 Sorted by residual: angle pdb=" N ARG A 678 " pdb=" CA ARG A 678 " pdb=" C ARG A 678 " ideal model delta sigma weight residual 112.93 105.68 7.25 1.12e+00 7.97e-01 4.19e+01 angle pdb=" N ARG C 678 " pdb=" CA ARG C 678 " pdb=" C ARG C 678 " ideal model delta sigma weight residual 112.93 105.69 7.24 1.12e+00 7.97e-01 4.17e+01 angle pdb=" C LEU C 267 " pdb=" N GLY C 268 " pdb=" CA GLY C 268 " ideal model delta sigma weight residual 123.08 117.67 5.41 1.12e+00 7.97e-01 2.33e+01 angle pdb=" C LEU A 267 " pdb=" N GLY A 268 " pdb=" CA GLY A 268 " ideal model delta sigma weight residual 123.08 117.71 5.37 1.12e+00 7.97e-01 2.30e+01 angle pdb=" CA PRO A 737 " pdb=" N PRO A 737 " pdb=" CD PRO A 737 " ideal model delta sigma weight residual 112.00 106.33 5.67 1.40e+00 5.10e-01 1.64e+01 ... (remaining 35073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13659 17.87 - 35.74: 1530 35.74 - 53.61: 440 53.61 - 71.48: 87 71.48 - 89.35: 30 Dihedral angle restraints: 15746 sinusoidal: 6842 harmonic: 8904 Sorted by residual: dihedral pdb=" CB CYS F 379 " pdb=" SG CYS F 379 " pdb=" SG CYS F 432 " pdb=" CB CYS F 432 " ideal model delta sinusoidal sigma weight residual 93.00 12.80 80.20 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 15.48 77.52 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS F 391 " pdb=" SG CYS F 391 " pdb=" SG CYS F 525 " pdb=" CB CYS F 525 " ideal model delta sinusoidal sigma weight residual 93.00 25.07 67.93 1 1.00e+01 1.00e-02 5.99e+01 ... (remaining 15743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3777 0.108 - 0.216: 115 0.216 - 0.324: 8 0.324 - 0.432: 0 0.432 - 0.540: 2 Chirality restraints: 3902 Sorted by residual: chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 131 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 131 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3899 not shown) Planarity restraints: 4390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 737 " 0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A 738 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 733 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO A 734 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 734 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 734 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 522 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C GLN A 522 " 0.032 2.00e-02 2.50e+03 pdb=" O GLN A 522 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE A 523 " -0.011 2.00e-02 2.50e+03 ... (remaining 4387 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 135 2.52 - 3.12: 19147 3.12 - 3.71: 37459 3.71 - 4.31: 53910 4.31 - 4.90: 89903 Nonbonded interactions: 200554 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.927 2.230 nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.928 2.230 nonbonded pdb=" O LEU D 113 " pdb=" OG SER D 116 " model vdw 2.206 2.440 nonbonded pdb=" O LEU B 113 " pdb=" OG SER B 116 " model vdw 2.206 2.440 nonbonded pdb=" O LEU D 121 " pdb=" OG SER D 124 " model vdw 2.212 2.440 ... (remaining 200549 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.030 Extract box with map and model: 6.660 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 67.970 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.350 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.008 0.130 25846 Z= 0.541 Angle : 0.805 11.459 35078 Z= 0.424 Chirality : 0.051 0.540 3902 Planarity : 0.004 0.082 4368 Dihedral : 16.438 89.352 10000 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.10 % Favored : 92.74 % Rotamer: Outliers : 4.43 % Allowed : 14.70 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -2.95 (0.13), residues: 3030 helix: -1.28 (0.11), residues: 1680 sheet: -1.40 (0.44), residues: 142 loop : -2.94 (0.15), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 111 HIS 0.008 0.001 HIS A 241 PHE 0.016 0.002 PHE D 295 TYR 0.018 0.002 TYR A 385 ARG 0.007 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 293 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 TYR cc_start: 0.8586 (m-10) cc_final: 0.8371 (m-10) REVERT: B 175 LEU cc_start: 0.7041 (mp) cc_final: 0.6818 (mp) REVERT: B 361 GLU cc_start: 0.8255 (pt0) cc_final: 0.7608 (tm-30) REVERT: B 446 MET cc_start: 0.7585 (tpp) cc_final: 0.7375 (mpp) REVERT: B 534 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.4244 (tp) REVERT: B 545 GLN cc_start: 0.7471 (mt0) cc_final: 0.6946 (mt0) REVERT: A 67 ASP cc_start: 0.7979 (m-30) cc_final: 0.7630 (m-30) REVERT: A 114 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8226 (mtpp) REVERT: A 270 MET cc_start: 0.9104 (tpp) cc_final: 0.8857 (tpp) REVERT: A 564 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8129 (mp0) REVERT: A 719 ASP cc_start: 0.8046 (t0) cc_final: 0.7712 (t0) REVERT: E 369 TYR cc_start: 0.6206 (t80) cc_final: 0.6003 (t80) REVERT: E 406 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7794 (mt-10) REVERT: E 432 CYS cc_start: 0.4689 (OUTLIER) cc_final: 0.4263 (m) REVERT: E 464 PHE cc_start: 0.8156 (m-80) cc_final: 0.7840 (m-80) REVERT: D 100 MET cc_start: 0.6372 (ptm) cc_final: 0.6119 (ptm) REVERT: D 135 TYR cc_start: 0.8620 (m-10) cc_final: 0.8374 (m-10) REVERT: D 361 GLU cc_start: 0.8317 (pt0) cc_final: 0.7664 (tm-30) REVERT: D 534 LEU cc_start: 0.5139 (OUTLIER) cc_final: 0.4226 (tp) REVERT: D 545 GLN cc_start: 0.7397 (mt0) cc_final: 0.6860 (mt0) REVERT: C 67 ASP cc_start: 0.8073 (m-30) cc_final: 0.7742 (m-30) REVERT: C 114 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8222 (mtpp) REVERT: C 270 MET cc_start: 0.9176 (tpp) cc_final: 0.8884 (tpp) REVERT: C 564 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8129 (mp0) REVERT: C 719 ASP cc_start: 0.8067 (t0) cc_final: 0.7699 (t0) REVERT: F 406 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7802 (mt-10) REVERT: F 432 CYS cc_start: 0.4948 (OUTLIER) cc_final: 0.4427 (m) REVERT: F 464 PHE cc_start: 0.8156 (m-80) cc_final: 0.7850 (m-80) outliers start: 117 outliers final: 75 residues processed: 398 average time/residue: 0.3507 time to fit residues: 220.4634 Evaluate side-chains 319 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 240 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 523 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 154 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 274 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 243 ASN ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 58 ASN A 98 GLN A 137 ASN A 159 ASN A 210 ASN A 239 HIS A 325 GLN A 401 HIS A 437 ASN A 472 GLN A 493 HIS A 505 HIS A 718 ASN A 735 ASN E 422 ASN D 71 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN D 243 ASN D 275 HIS ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 98 GLN C 137 ASN C 159 ASN C 210 ASN C 239 HIS C 325 GLN C 401 HIS C 437 ASN C 472 GLN C 493 HIS C 505 HIS F 422 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25846 Z= 0.159 Angle : 0.590 9.430 35078 Z= 0.291 Chirality : 0.042 0.334 3902 Planarity : 0.004 0.067 4368 Dihedral : 11.076 77.256 4509 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.55 % Rotamer: Outliers : 3.52 % Allowed : 17.61 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -1.50 (0.15), residues: 3030 helix: 0.04 (0.13), residues: 1666 sheet: -1.23 (0.44), residues: 142 loop : -2.44 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 391 HIS 0.004 0.001 HIS B 132 PHE 0.012 0.001 PHE D 117 TYR 0.044 0.001 TYR B 21 ARG 0.005 0.000 ARG F 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 262 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 534 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4283 (tp) REVERT: B 537 GLN cc_start: 0.6461 (OUTLIER) cc_final: 0.6033 (mt0) REVERT: A 67 ASP cc_start: 0.7845 (m-30) cc_final: 0.7466 (m-30) REVERT: A 325 GLN cc_start: 0.8240 (tm130) cc_final: 0.7733 (tp-100) REVERT: A 596 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8944 (mtpt) REVERT: A 719 ASP cc_start: 0.7721 (t0) cc_final: 0.7469 (t0) REVERT: E 369 TYR cc_start: 0.6120 (t80) cc_final: 0.5822 (t80) REVERT: E 392 PHE cc_start: 0.7413 (p90) cc_final: 0.7126 (p90) REVERT: E 406 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7878 (mt-10) REVERT: E 464 PHE cc_start: 0.8111 (m-80) cc_final: 0.7746 (m-80) REVERT: D 69 MET cc_start: 0.6544 (tpt) cc_final: 0.6052 (tpt) REVERT: D 281 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6934 (mp) REVERT: D 380 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 385 MET cc_start: 0.7558 (mtm) cc_final: 0.7346 (mtm) REVERT: D 390 LEU cc_start: 0.6646 (tt) cc_final: 0.6441 (tt) REVERT: D 534 LEU cc_start: 0.4911 (OUTLIER) cc_final: 0.4062 (tp) REVERT: D 537 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.6054 (mt0) REVERT: C 67 ASP cc_start: 0.7986 (m-30) cc_final: 0.7589 (m-30) REVERT: C 325 GLN cc_start: 0.8223 (tm130) cc_final: 0.7715 (tp-100) REVERT: C 596 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8957 (mtpt) REVERT: C 719 ASP cc_start: 0.7765 (t0) cc_final: 0.7505 (t0) REVERT: F 369 TYR cc_start: 0.6646 (t80) cc_final: 0.6254 (t80) REVERT: F 392 PHE cc_start: 0.7439 (p90) cc_final: 0.7186 (p90) REVERT: F 406 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7899 (mt-10) REVERT: F 464 PHE cc_start: 0.8163 (m-80) cc_final: 0.7834 (m-80) REVERT: F 493 ARG cc_start: 0.8488 (mmt-90) cc_final: 0.8210 (mmt90) outliers start: 93 outliers final: 55 residues processed: 343 average time/residue: 0.3329 time to fit residues: 185.9340 Evaluate side-chains 303 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 241 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain F residue 379 CYS Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 274 optimal weight: 0.0980 chunk 296 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 220 optimal weight: 0.1980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 378 HIS A 735 ASN ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25846 Z= 0.180 Angle : 0.567 9.961 35078 Z= 0.278 Chirality : 0.042 0.265 3902 Planarity : 0.004 0.047 4368 Dihedral : 9.918 76.974 4444 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.97 % Favored : 93.89 % Rotamer: Outliers : 4.02 % Allowed : 18.07 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.98 (0.15), residues: 3030 helix: 0.47 (0.13), residues: 1666 sheet: -1.01 (0.44), residues: 142 loop : -2.22 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 478 HIS 0.013 0.001 HIS C 34 PHE 0.012 0.001 PHE A 684 TYR 0.027 0.001 TYR B 21 ARG 0.004 0.000 ARG F 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 256 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 LEU cc_start: 0.7262 (mp) cc_final: 0.7059 (mp) REVERT: B 363 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7195 (mt-10) REVERT: B 380 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7170 (tm-30) REVERT: B 504 TYR cc_start: 0.5913 (t80) cc_final: 0.5703 (t80) REVERT: B 534 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.4245 (tp) REVERT: B 537 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.6023 (mt0) REVERT: A 67 ASP cc_start: 0.7888 (m-30) cc_final: 0.7495 (m-30) REVERT: A 256 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9297 (mm) REVERT: A 325 GLN cc_start: 0.8287 (tm130) cc_final: 0.7771 (tp-100) REVERT: A 596 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8760 (mtpt) REVERT: A 719 ASP cc_start: 0.7854 (t0) cc_final: 0.7495 (t0) REVERT: E 369 TYR cc_start: 0.6469 (t80) cc_final: 0.6179 (t80) REVERT: E 392 PHE cc_start: 0.7448 (p90) cc_final: 0.7242 (p90) REVERT: E 406 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7897 (mt-10) REVERT: E 454 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.7955 (ttm170) REVERT: E 464 PHE cc_start: 0.8044 (m-80) cc_final: 0.7675 (m-80) REVERT: D 69 MET cc_start: 0.6666 (tpt) cc_final: 0.6208 (tpt) REVERT: D 281 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6861 (mp) REVERT: D 363 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: D 380 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7614 (tm-30) REVERT: D 385 MET cc_start: 0.7480 (mtm) cc_final: 0.7249 (mtm) REVERT: D 476 GLU cc_start: 0.6423 (mt-10) cc_final: 0.6194 (mm-30) REVERT: D 534 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4146 (tp) REVERT: D 537 GLN cc_start: 0.6388 (OUTLIER) cc_final: 0.5992 (mt0) REVERT: C 35 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7796 (mt-10) REVERT: C 67 ASP cc_start: 0.7910 (m-30) cc_final: 0.7531 (m-30) REVERT: C 183 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.8950 (t80) REVERT: C 256 ILE cc_start: 0.9622 (OUTLIER) cc_final: 0.9313 (mm) REVERT: C 325 GLN cc_start: 0.8270 (tm130) cc_final: 0.7782 (tp-100) REVERT: C 596 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8751 (mtpt) REVERT: C 719 ASP cc_start: 0.7802 (t0) cc_final: 0.7521 (t0) REVERT: F 369 TYR cc_start: 0.6659 (t80) cc_final: 0.6273 (t80) REVERT: F 406 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7984 (mt-10) REVERT: F 464 PHE cc_start: 0.8125 (m-80) cc_final: 0.7794 (m-80) outliers start: 106 outliers final: 73 residues processed: 345 average time/residue: 0.3365 time to fit residues: 189.9339 Evaluate side-chains 328 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 243 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 379 CYS Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 ASN ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 277 ASN D 410 ASN ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25846 Z= 0.228 Angle : 0.573 10.292 35078 Z= 0.282 Chirality : 0.042 0.263 3902 Planarity : 0.004 0.046 4368 Dihedral : 9.600 76.548 4444 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.84 % Favored : 94.03 % Rotamer: Outliers : 4.09 % Allowed : 19.02 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.78 (0.15), residues: 3030 helix: 0.62 (0.13), residues: 1664 sheet: -0.92 (0.44), residues: 142 loop : -2.10 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 391 HIS 0.004 0.001 HIS C 241 PHE 0.014 0.001 PHE F 392 TYR 0.053 0.001 TYR D 21 ARG 0.006 0.000 ARG F 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 251 time to evaluate : 2.442 Fit side-chains revert: symmetry clash REVERT: B 363 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: B 380 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7388 (tm-30) REVERT: B 504 TYR cc_start: 0.5906 (t80) cc_final: 0.5385 (t80) REVERT: B 508 MET cc_start: 0.7573 (mmm) cc_final: 0.6863 (mtt) REVERT: B 534 LEU cc_start: 0.5208 (OUTLIER) cc_final: 0.4324 (tp) REVERT: B 537 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.6056 (mt0) REVERT: B 545 GLN cc_start: 0.7454 (mt0) cc_final: 0.6777 (mt0) REVERT: A 67 ASP cc_start: 0.7934 (m-30) cc_final: 0.7539 (m-30) REVERT: A 256 ILE cc_start: 0.9631 (OUTLIER) cc_final: 0.9333 (mm) REVERT: A 325 GLN cc_start: 0.8315 (tm130) cc_final: 0.7826 (tp-100) REVERT: A 383 MET cc_start: 0.9048 (mtp) cc_final: 0.8751 (mtp) REVERT: A 431 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7580 (p0) REVERT: A 719 ASP cc_start: 0.7962 (t0) cc_final: 0.7590 (t0) REVERT: E 392 PHE cc_start: 0.7456 (p90) cc_final: 0.7253 (p90) REVERT: E 406 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7911 (mt-10) REVERT: E 454 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8010 (ttm170) REVERT: E 464 PHE cc_start: 0.7962 (m-80) cc_final: 0.7626 (m-80) REVERT: D 281 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6902 (mp) REVERT: D 344 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7235 (p90) REVERT: D 363 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: D 380 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7620 (tm-30) REVERT: D 451 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: D 476 GLU cc_start: 0.6486 (mt-10) cc_final: 0.6248 (mm-30) REVERT: D 503 TRP cc_start: 0.3604 (m100) cc_final: 0.3099 (m-90) REVERT: D 534 LEU cc_start: 0.5005 (OUTLIER) cc_final: 0.4155 (tp) REVERT: D 537 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.6003 (mt0) REVERT: D 545 GLN cc_start: 0.7261 (mt0) cc_final: 0.6592 (mt0) REVERT: C 67 ASP cc_start: 0.7909 (m-30) cc_final: 0.7518 (m-30) REVERT: C 256 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9331 (mm) REVERT: C 325 GLN cc_start: 0.8275 (tm130) cc_final: 0.7781 (tp-100) REVERT: C 383 MET cc_start: 0.9067 (mtp) cc_final: 0.8752 (mtp) REVERT: C 431 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7570 (p0) REVERT: C 719 ASP cc_start: 0.7947 (t0) cc_final: 0.7582 (t0) REVERT: F 369 TYR cc_start: 0.6616 (t80) cc_final: 0.6238 (t80) REVERT: F 406 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7893 (mt-10) REVERT: F 464 PHE cc_start: 0.8102 (m-80) cc_final: 0.7771 (m-80) outliers start: 108 outliers final: 78 residues processed: 336 average time/residue: 0.3277 time to fit residues: 179.1280 Evaluate side-chains 332 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 241 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain F residue 379 CYS Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9645 > 50: distance: 21 - 60: 6.944 distance: 48 - 60: 10.235 distance: 60 - 61: 22.404 distance: 61 - 62: 20.308 distance: 61 - 64: 29.727 distance: 62 - 63: 15.978 distance: 62 - 72: 31.156 distance: 64 - 65: 14.484 distance: 65 - 66: 13.649 distance: 65 - 67: 42.301 distance: 66 - 68: 35.228 distance: 67 - 69: 40.555 distance: 68 - 70: 34.215 distance: 69 - 70: 20.573 distance: 70 - 71: 14.617 distance: 72 - 73: 17.703 distance: 73 - 76: 25.623 distance: 76 - 77: 21.804 distance: 77 - 78: 22.327 distance: 78 - 79: 17.028 distance: 79 - 80: 55.205 distance: 80 - 81: 44.624 distance: 80 - 82: 39.758 distance: 83 - 84: 52.956 distance: 84 - 85: 17.182 distance: 84 - 87: 33.224 distance: 85 - 86: 42.031 distance: 88 - 89: 38.009 distance: 89 - 90: 36.999 distance: 90 - 91: 43.809 distance: 92 - 93: 12.450 distance: 93 - 94: 8.856 distance: 93 - 96: 24.638 distance: 94 - 95: 30.498 distance: 94 - 99: 8.019 distance: 96 - 97: 5.167 distance: 96 - 98: 15.655 distance: 99 - 100: 31.706 distance: 100 - 101: 8.777 distance: 100 - 103: 8.329 distance: 101 - 102: 24.594 distance: 103 - 104: 23.258 distance: 104 - 105: 28.290 distance: 104 - 106: 17.095 distance: 107 - 108: 37.533 distance: 108 - 109: 16.867 distance: 108 - 111: 20.931 distance: 109 - 110: 7.560 distance: 109 - 115: 31.608 distance: 111 - 112: 25.968 distance: 112 - 113: 3.909 distance: 112 - 114: 12.895 distance: 115 - 116: 6.298 distance: 116 - 117: 13.317 distance: 116 - 119: 15.258 distance: 117 - 118: 41.415 distance: 117 - 123: 41.598 distance: 119 - 120: 18.186 distance: 119 - 121: 19.372 distance: 120 - 122: 25.446 distance: 123 - 124: 25.048 distance: 124 - 125: 33.709 distance: 124 - 127: 34.868 distance: 125 - 126: 35.027 distance: 125 - 129: 38.982 distance: 127 - 128: 29.117 distance: 129 - 130: 37.742 distance: 130 - 131: 44.461 distance: 130 - 133: 40.014 distance: 131 - 132: 48.949 distance: 131 - 136: 32.217 distance: 133 - 134: 6.744 distance: 134 - 135: 8.883 distance: 136 - 137: 13.020 distance: 137 - 138: 23.285 distance: 137 - 140: 30.463 distance: 138 - 139: 40.854 distance: 138 - 142: 18.301