Starting phenix.real_space_refine on Fri Aug 9 06:56:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/08_2024/6m17_30039.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/08_2024/6m17_30039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/08_2024/6m17_30039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/08_2024/6m17_30039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/08_2024/6m17_30039.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/08_2024/6m17_30039.cif" } resolution = 2.9 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 142 5.16 5 C 16396 2.51 5 N 4054 2.21 5 O 4750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ARG 518": "NH1" <-> "NH2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B ARG 671": "NH1" <-> "NH2" Residue "B ARG 678": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E ARG 408": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C GLU 437": "OE1" <-> "OE2" Residue "C GLU 501": "OE1" <-> "OE2" Residue "C GLU 553": "OE1" <-> "OE2" Residue "C GLU 569": "OE1" <-> "OE2" Residue "C ARG 607": "NH1" <-> "NH2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 639": "OE1" <-> "OE2" Residue "D ARG 671": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F ARG 408": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25344 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "B" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6089 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 35, 'TRANS': 712} Chain: "E" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "C" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "D" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6089 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 35, 'TRANS': 712} Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" 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: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 14.03, per 1000 atoms: 0.55 Number of scatterers: 25344 At special positions: 0 Unit cell: (114.135, 148.919, 214.139, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 142 16.00 O 4750 8.00 N 4054 7.00 C 16396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.66 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.17 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.54 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.37 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 383 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.66 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.17 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.54 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.04 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.37 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 N 2 " - " NAG N 3 " " 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 V 2 " - " NAG V 3 " NAG-ASN " NAG A 701 " - " ASN A 158 " " NAG A 702 " - " ASN A 182 " " NAG A 703 " - " ASN A 354 " " NAG A 704 " - " ASN A 368 " " NAG B 901 " - " ASN B 322 " " NAG C 701 " - " ASN C 158 " " NAG C 702 " - " ASN C 182 " " NAG C 703 " - " ASN C 354 " " NAG C 704 " - " ASN C 368 " " NAG D 901 " - " ASN D 322 " " NAG G 1 " - " ASN A 258 " " NAG H 1 " - " ASN B 53 " " NAG I 1 " - " ASN B 90 " " NAG J 1 " - " ASN B 103 " " NAG K 1 " - " ASN B 432 " " NAG L 1 " - " ASN B 546 " " NAG M 1 " - " ASN B 690 " " NAG N 1 " - " ASN E 343 " " NAG O 1 " - " ASN C 258 " " NAG P 1 " - " ASN D 53 " " NAG Q 1 " - " ASN D 90 " " NAG R 1 " - " ASN D 103 " " NAG S 1 " - " ASN D 432 " " NAG T 1 " - " ASN D 546 " " NAG U 1 " - " ASN D 690 " " NAG V 1 " - " ASN F 343 " Time building additional restraints: 10.48 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 374 " pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" NE2 HIS D 374 " 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 14 sheets defined 59.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.860A pdb=" N TYR A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 4.244A pdb=" N SER A 64 " --> pdb=" O TYR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 81 Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.651A pdb=" N ALA A 91 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.721A pdb=" N TRP A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 142 removed outlier: 3.551A pdb=" N SER A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.589A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.977A pdb=" N CYS A 200 " --> pdb=" O TRP A 196 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 242 removed outlier: 3.733A pdb=" N ALA A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.728A pdb=" N THR A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.629A pdb=" N GLN A 264 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.528A pdb=" N ASP A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 removed outlier: 3.838A pdb=" N SER A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 317 removed outlier: 3.625A pdb=" N SER A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 346 removed outlier: 3.771A pdb=" N SER A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 371 removed outlier: 4.406A pdb=" N GLN A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 4.014A pdb=" N THR A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.511A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 420 " --> pdb=" O TRP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 445 removed outlier: 4.267A pdb=" N GLY A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 454 through 470 removed outlier: 4.023A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 477 through 507 removed outlier: 3.640A pdb=" N LEU A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) Proline residue: A 493 - end of helix removed outlier: 3.783A pdb=" N ILE A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 497 " --> pdb=" O PRO A 493 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 522 removed outlier: 3.873A pdb=" N LYS A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.596A pdb=" N THR A 533 " --> pdb=" O PHE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 546 removed outlier: 3.767A pdb=" N LEU A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 554 removed outlier: 4.202A pdb=" N PHE A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 609 removed outlier: 3.879A pdb=" N VAL A 585 " --> pdb=" O TRP A 581 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 3.837A pdb=" N ILE A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix Processing helix chain 'B' and resid 22 through 53 removed outlier: 3.814A pdb=" N LYS B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 81 removed outlier: 3.756A pdb=" N ASN B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.640A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 129 removed outlier: 3.688A pdb=" N LYS B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 removed outlier: 3.528A pdb=" N ILE B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 193 removed outlier: 3.608A pdb=" N TRP B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.883A pdb=" N VAL B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 205 through 208 removed outlier: 3.565A pdb=" N GLU B 208 " --> pdb=" O GLY B 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 removed outlier: 4.309A pdb=" N ILE B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.759A pdb=" N SER B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 383 removed outlier: 3.636A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 removed outlier: 3.548A pdb=" N ARG B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.552A pdb=" N ALA B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 412 " --> pdb=" O MET B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 444 removed outlier: 3.597A pdb=" N GLU B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 465 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.751A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 502 removed outlier: 3.593A pdb=" N SER B 502 " --> pdb=" O ASP B 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 502' Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.878A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 520 " --> pdb=" O TYR B 516 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 548 through 559 removed outlier: 4.396A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 removed outlier: 3.675A pdb=" N GLU B 571 " --> pdb=" O THR B 567 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 removed outlier: 3.577A pdb=" N TYR B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.576A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.643A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 removed outlier: 3.606A pdb=" N MET B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.502A pdb=" N SER B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 716 removed outlier: 3.570A pdb=" N ASP B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 766 removed outlier: 3.933A pdb=" N ILE B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 758 " --> pdb=" O VAL B 754 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 344 Processing helix chain 'E' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.867A pdb=" N TYR E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.860A pdb=" N TYR C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 4.244A pdb=" N SER C 64 " --> pdb=" O TYR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 81 through 97 removed outlier: 3.651A pdb=" N ALA C 91 " --> pdb=" O TYR C 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 93 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 96 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.721A pdb=" N TRP C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 142 removed outlier: 3.551A pdb=" N SER C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR C 128 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 133 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 134 " --> pdb=" O ASN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.589A pdb=" N ARG C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 195 through 212 removed outlier: 3.977A pdb=" N CYS C 200 " --> pdb=" O TRP C 196 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 201 " --> pdb=" O MET C 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 242 removed outlier: 3.733A pdb=" N ALA C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 228 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 3.728A pdb=" N THR C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 256 Processing helix chain 'C' and resid 258 through 264 removed outlier: 3.629A pdb=" N GLN C 264 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 279 removed outlier: 3.528A pdb=" N ASP C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 291 removed outlier: 3.838A pdb=" N SER C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 317 removed outlier: 3.625A pdb=" N SER C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 346 removed outlier: 3.771A pdb=" N SER C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 removed outlier: 4.406A pdb=" N GLN C 365 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 4.014A pdb=" N THR C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 430 removed outlier: 3.511A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 420 " --> pdb=" O TRP C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 445 removed outlier: 4.267A pdb=" N GLY C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 435 " --> pdb=" O SER C 431 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 437 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 439 " --> pdb=" O ASN C 435 " (cutoff:3.500A) Proline residue: C 442 - end of helix Processing helix chain 'C' and resid 454 through 470 removed outlier: 4.023A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 460 " --> pdb=" O GLU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 474 Processing helix chain 'C' and resid 477 through 507 removed outlier: 3.640A pdb=" N LEU C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 484 " --> pdb=" O TYR C 480 " (cutoff:3.500A) Proline residue: C 493 - end of helix removed outlier: 3.783A pdb=" N ILE C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 497 " --> pdb=" O PRO C 493 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 522 removed outlier: 3.873A pdb=" N LYS C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 517 " --> pdb=" O ARG C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 536 removed outlier: 3.596A pdb=" N THR C 533 " --> pdb=" O PHE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 546 removed outlier: 3.767A pdb=" N LEU C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 554 removed outlier: 4.202A pdb=" N PHE C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 554 " --> pdb=" O PHE C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 609 removed outlier: 3.879A pdb=" N VAL C 585 " --> pdb=" O TRP C 581 " (cutoff:3.500A) Proline residue: C 593 - end of helix removed outlier: 3.837A pdb=" N ILE C 597 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Proline residue: C 598 - end of helix Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.814A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.756A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.640A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.688A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.528A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 193 removed outlier: 3.608A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.883A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.565A pdb=" N GLU D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.309A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.759A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.636A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.548A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.552A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.597A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.751A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.593A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.878A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.396A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.675A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.577A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.576A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.643A pdb=" N ALA D 627 " --> pdb=" O SER D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 658 removed outlier: 3.606A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.502A pdb=" N SER D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 716 removed outlier: 3.570A pdb=" N ASP D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 715 " --> pdb=" O ILE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 766 removed outlier: 3.933A pdb=" N ILE D 744 " --> pdb=" O SER D 740 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 758 " --> pdb=" O VAL D 754 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE D 762 " --> pdb=" O VAL D 758 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY D 764 " --> pdb=" O LEU D 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 344 Processing helix chain 'F' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP F 389 " --> pdb=" O LYS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.867A pdb=" N TYR F 421 " --> pdb=" O LYS F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 559 through 562 removed outlier: 4.380A pdb=" N GLN A 574 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 132 through 134 removed outlier: 10.037A pdb=" N VAL B 132 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLN B 139 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN B 134 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.029A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 352 removed outlier: 3.582A pdb=" N LEU B 351 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AA6, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR E 449 " --> pdb=" O PHE E 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE E 497 " --> pdb=" O TYR E 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR E 451 " --> pdb=" O TYR E 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 559 through 562 removed outlier: 4.380A pdb=" N GLN C 574 " --> pdb=" O ILE C 562 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 132 through 134 removed outlier: 10.037A pdb=" N VAL D 132 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLN D 139 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN D 134 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.029A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.582A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 670 through 673 Processing sheet with id=AB4, first strand: chain 'F' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR F 449 " --> pdb=" O PHE F 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE F 497 " --> pdb=" O TYR F 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR F 451 " --> pdb=" O TYR F 495 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 3072 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: 7.21 Time building geometry restraints manager: 11.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4822 1.33 - 1.45: 7124 1.45 - 1.58: 13852 1.58 - 1.70: 0 1.70 - 1.82: 224 Bond restraints: 26022 Sorted by residual: bond pdb=" N PRO D 135 " pdb=" CD PRO D 135 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N PRO B 135 " pdb=" CD PRO B 135 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N PRO B 677 " pdb=" CD PRO B 677 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" N PRO D 677 " pdb=" CD PRO D 677 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" N PRO C 73 " pdb=" CD PRO C 73 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 ... (remaining 26017 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.84: 892 106.84 - 114.74: 15054 114.74 - 122.65: 16734 122.65 - 130.55: 2576 130.55 - 138.45: 158 Bond angle restraints: 35414 Sorted by residual: angle pdb=" N GLU A 157 " pdb=" CA GLU A 157 " pdb=" C GLU A 157 " ideal model delta sigma weight residual 111.03 99.23 11.80 1.11e+00 8.12e-01 1.13e+02 angle pdb=" N GLU C 157 " pdb=" CA GLU C 157 " pdb=" C GLU C 157 " ideal model delta sigma weight residual 111.03 99.23 11.80 1.11e+00 8.12e-01 1.13e+02 angle pdb=" N LEU D 143 " pdb=" CA LEU D 143 " pdb=" C LEU D 143 " ideal model delta sigma weight residual 107.62 120.24 -12.62 1.97e+00 2.58e-01 4.11e+01 angle pdb=" N LEU B 143 " pdb=" CA LEU B 143 " pdb=" C LEU B 143 " ideal model delta sigma weight residual 107.62 120.24 -12.62 1.97e+00 2.58e-01 4.11e+01 angle pdb=" N LEU B 144 " pdb=" CA LEU B 144 " pdb=" C LEU B 144 " ideal model delta sigma weight residual 110.80 124.18 -13.38 2.13e+00 2.20e-01 3.95e+01 ... (remaining 35409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 13920 17.68 - 35.37: 1402 35.37 - 53.05: 366 53.05 - 70.74: 102 70.74 - 88.42: 34 Dihedral angle restraints: 15824 sinusoidal: 6850 harmonic: 8974 Sorted by residual: dihedral pdb=" CA TYR E 421 " pdb=" C TYR E 421 " pdb=" N ASN E 422 " pdb=" CA ASN E 422 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA TYR F 421 " pdb=" C TYR F 421 " pdb=" N ASN F 422 " pdb=" CA ASN F 422 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CB CYS F 336 " pdb=" SG CYS F 336 " pdb=" SG CYS F 361 " pdb=" CB CYS F 361 " ideal model delta sinusoidal sigma weight residual -86.00 -39.27 -46.73 1 1.00e+01 1.00e-02 3.02e+01 ... (remaining 15821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 3956 0.281 - 0.562: 14 0.562 - 0.842: 6 0.842 - 1.123: 0 1.123 - 1.404: 4 Chirality restraints: 3980 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.00 -1.40 2.00e-02 2.50e+03 4.93e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.00 -1.40 2.00e-02 2.50e+03 4.93e+03 chirality pdb=" C1 NAG V 3 " pdb=" O4 NAG V 2 " pdb=" C2 NAG V 3 " pdb=" O5 NAG V 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-02 2.50e+03 1.00e+03 ... (remaining 3977 not shown) Planarity restraints: 4478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG J 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG R 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 2 " 0.294 2.00e-02 2.50e+03 2.53e-01 7.98e+02 pdb=" C7 NAG V 2 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG V 2 " -0.008 2.00e-02 2.50e+03 pdb=" N2 NAG V 2 " -0.430 2.00e-02 2.50e+03 pdb=" O7 NAG V 2 " 0.209 2.00e-02 2.50e+03 ... (remaining 4475 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 164 2.53 - 3.12: 18176 3.12 - 3.71: 37393 3.71 - 4.31: 55151 4.31 - 4.90: 90421 Nonbonded interactions: 201305 Sorted by model distance: nonbonded pdb=" O SER B 105 " pdb=" OG SER B 106 " model vdw 1.932 3.040 nonbonded pdb=" O SER D 105 " pdb=" OG SER D 106 " model vdw 1.932 3.040 nonbonded pdb=" NH1 ARG F 346 " pdb=" O PHE F 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG E 346 " pdb=" O PHE E 347 " model vdw 1.982 3.120 nonbonded pdb=" O SER F 477 " pdb=" OG1 THR F 478 " model vdw 2.032 3.040 ... (remaining 201300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'N' 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.250 Process input model: 69.050 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 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 0.075 26022 Z= 0.521 Angle : 1.048 13.454 35414 Z= 0.622 Chirality : 0.081 1.404 3980 Planarity : 0.014 0.305 4452 Dihedral : 15.887 88.421 10016 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 1.70 % Allowed : 9.48 % Favored : 88.82 % Rotamer: Outliers : 5.25 % Allowed : 9.39 % Favored : 85.37 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.89 (0.10), residues: 3060 helix: -4.47 (0.05), residues: 1608 sheet: -1.10 (0.39), residues: 160 loop : -3.34 (0.14), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 302 HIS 0.006 0.001 HIS D 241 PHE 0.016 0.002 PHE C 48 TYR 0.024 0.002 TYR B 385 ARG 0.005 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 573 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLN cc_start: 0.6201 (OUTLIER) cc_final: 0.5725 (tm130) REVERT: A 221 LYS cc_start: 0.4003 (OUTLIER) cc_final: 0.3636 (ttmm) REVERT: A 355 VAL cc_start: 0.8526 (t) cc_final: 0.7838 (p) REVERT: A 502 MET cc_start: 0.6348 (tpp) cc_final: 0.6014 (mmt) REVERT: B 102 GLN cc_start: 0.8042 (tp40) cc_final: 0.7454 (pm20) REVERT: B 190 MET cc_start: 0.7968 (tmm) cc_final: 0.7683 (tmm) REVERT: B 228 HIS cc_start: 0.7021 (t70) cc_final: 0.6692 (m-70) REVERT: B 313 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8454 (tptt) REVERT: B 408 MET cc_start: 0.8774 (mmt) cc_final: 0.8544 (mmt) REVERT: B 556 ASN cc_start: 0.8524 (t0) cc_final: 0.7989 (t0) REVERT: B 637 ASP cc_start: 0.8174 (p0) cc_final: 0.7801 (m-30) REVERT: B 651 MET cc_start: 0.8884 (mmm) cc_final: 0.8523 (mmt) REVERT: B 736 GLN cc_start: 0.5057 (OUTLIER) cc_final: 0.3900 (tt0) REVERT: E 469 SER cc_start: 0.7193 (OUTLIER) cc_final: 0.6581 (t) REVERT: C 159 GLN cc_start: 0.6201 (OUTLIER) cc_final: 0.5725 (tm130) REVERT: C 221 LYS cc_start: 0.4004 (OUTLIER) cc_final: 0.3636 (ttmm) REVERT: C 355 VAL cc_start: 0.8524 (t) cc_final: 0.7834 (p) REVERT: C 502 MET cc_start: 0.6351 (tpp) cc_final: 0.6013 (mmt) REVERT: D 102 GLN cc_start: 0.8044 (tp40) cc_final: 0.7453 (pm20) REVERT: D 190 MET cc_start: 0.7967 (tmm) cc_final: 0.7684 (tmm) REVERT: D 228 HIS cc_start: 0.7022 (t70) cc_final: 0.6692 (m-70) REVERT: D 313 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8452 (tptt) REVERT: D 408 MET cc_start: 0.8779 (mmt) cc_final: 0.8550 (mmt) REVERT: D 556 ASN cc_start: 0.8524 (t0) cc_final: 0.7991 (t0) REVERT: D 637 ASP cc_start: 0.8172 (p0) cc_final: 0.7802 (m-30) REVERT: D 651 MET cc_start: 0.8885 (mmm) cc_final: 0.8525 (mmt) REVERT: D 736 GLN cc_start: 0.5061 (OUTLIER) cc_final: 0.3905 (tt0) REVERT: F 469 SER cc_start: 0.7194 (OUTLIER) cc_final: 0.6586 (t) outliers start: 142 outliers final: 12 residues processed: 677 average time/residue: 1.2006 time to fit residues: 952.8914 Evaluate side-chains 272 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain F residue 489 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 123 optimal weight: 0.4980 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 194 GLN A 310 ASN A 340 ASN A 435 ASN A 531 GLN A 580 ASN B 51 ASN B 58 ASN B 61 ASN B 96 GLN B 101 GLN B 159 ASN B 175 GLN B 239 HIS B 277 ASN B 287 GLN B 378 HIS B 437 ASN B 472 GLN B 505 HIS B 586 ASN B 736 GLN E 394 ASN E 422 ASN E 440 ASN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS C 194 GLN C 310 ASN C 340 ASN C 435 ASN C 531 GLN C 580 ASN D 51 ASN D 58 ASN D 61 ASN D 96 GLN D 101 GLN D 159 ASN D 175 GLN D 239 HIS D 277 ASN D 287 GLN D 378 HIS D 437 ASN D 472 GLN D 505 HIS D 586 ASN D 736 GLN F 394 ASN F 422 ASN F 440 ASN ** F 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26022 Z= 0.261 Angle : 0.790 12.849 35414 Z= 0.398 Chirality : 0.051 0.528 3980 Planarity : 0.006 0.047 4452 Dihedral : 8.518 86.032 4294 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.20 % Favored : 94.54 % Rotamer: Outliers : 3.88 % Allowed : 17.15 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.13), residues: 3060 helix: -2.24 (0.10), residues: 1708 sheet: -0.67 (0.47), residues: 118 loop : -2.62 (0.16), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 436 HIS 0.007 0.001 HIS D 34 PHE 0.024 0.002 PHE E 429 TYR 0.024 0.002 TYR A 316 ARG 0.007 0.001 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 313 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7914 (mm-40) REVERT: A 583 TYR cc_start: 0.6774 (OUTLIER) cc_final: 0.6220 (m-80) REVERT: B 102 GLN cc_start: 0.8221 (tp40) cc_final: 0.7726 (pm20) REVERT: B 190 MET cc_start: 0.7977 (tmm) cc_final: 0.7679 (tmm) REVERT: B 293 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.7982 (p) REVERT: B 297 MET cc_start: 0.7919 (mtp) cc_final: 0.7491 (mtm) REVERT: B 313 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8548 (tptt) REVERT: B 556 ASN cc_start: 0.8305 (t0) cc_final: 0.7808 (t0) REVERT: B 651 MET cc_start: 0.8801 (mmm) cc_final: 0.8479 (mmt) REVERT: B 680 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8542 (p) REVERT: B 692 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.8032 (t) REVERT: B 736 GLN cc_start: 0.4971 (OUTLIER) cc_final: 0.3940 (tt0) REVERT: C 365 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7913 (mm-40) REVERT: C 583 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: D 102 GLN cc_start: 0.8223 (tp40) cc_final: 0.7728 (pm20) REVERT: D 190 MET cc_start: 0.7980 (tmm) cc_final: 0.7680 (tmm) REVERT: D 293 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.7979 (p) REVERT: D 297 MET cc_start: 0.7928 (mtp) cc_final: 0.7498 (mtm) REVERT: D 313 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8547 (tptt) REVERT: D 556 ASN cc_start: 0.8304 (t0) cc_final: 0.7807 (t0) REVERT: D 651 MET cc_start: 0.8803 (mmm) cc_final: 0.8484 (mmt) REVERT: D 680 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8542 (p) REVERT: D 692 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.8037 (t) REVERT: D 736 GLN cc_start: 0.4974 (OUTLIER) cc_final: 0.3945 (tt0) outliers start: 105 outliers final: 36 residues processed: 385 average time/residue: 1.0925 time to fit residues: 505.5672 Evaluate side-chains 285 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 237 time to evaluate : 4.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 298 optimal weight: 0.5980 chunk 246 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 175 GLN B 228 HIS B 599 ASN E 487 ASN C 435 ASN D 175 GLN D 228 HIS D 599 ASN F 487 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.3658 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: