Starting phenix.real_space_refine on Mon Feb 19 17:10:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/02_2024/6m17_30039.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/02_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_30039/02_2024/6m17_30039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/02_2024/6m17_30039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/02_2024/6m17_30039.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m17_30039/02_2024/6m17_30039.pdb" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12.11, per 1000 atoms: 0.48 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: 10.60 Conformation dependent library (CDL) restraints added in 5.2 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: 2.73 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: 8.15 Time building geometry restraints manager: 11.45 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 2.440 nonbonded pdb=" O SER D 105 " pdb=" OG SER D 106 " model vdw 1.932 2.440 nonbonded pdb=" NH1 ARG F 346 " pdb=" O PHE F 347 " model vdw 1.982 2.520 nonbonded pdb=" NH1 ARG E 346 " pdb=" O PHE E 347 " model vdw 1.982 2.520 nonbonded pdb=" O SER F 477 " pdb=" OG1 THR F 478 " model vdw 2.032 2.440 ... (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 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: 6.470 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 70.220 Find NCS groups from input model: 1.410 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: 0.010 Load rotamer database and sin/cos tables:17.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.890 ------------------------------------------------------------------------------- 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 : 3.005 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: 1.1715 time to fit residues: 927.4629 Evaluate side-chains 272 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 2.729 ------------------------------------------------------------------------------- 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: 1.9990 chunk 78 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 276 optimal weight: 0.2980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 108 HIS A 194 GLN A 310 ASN A 340 ASN A 435 ASN A 479 GLN 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 360 ASN E 394 ASN E 422 ASN E 440 ASN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN C 108 HIS C 194 GLN C 310 ASN C 340 ASN C 435 ASN C 479 GLN 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 360 ASN F 394 ASN F 422 ASN F 440 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26022 Z= 0.262 Angle : 0.790 12.026 35414 Z= 0.395 Chirality : 0.050 0.445 3980 Planarity : 0.006 0.048 4452 Dihedral : 8.631 85.883 4294 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.49 % Favored : 94.18 % Rotamer: Outliers : 4.25 % Allowed : 17.89 % Favored : 77.86 % 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: -3.58 (0.13), residues: 3060 helix: -2.23 (0.10), residues: 1686 sheet: -0.66 (0.47), residues: 118 loop : -2.61 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 436 HIS 0.008 0.001 HIS D 34 PHE 0.024 0.002 PHE D 746 TYR 0.025 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 409 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 294 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7874 (mm-40) REVERT: A 583 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: B 102 GLN cc_start: 0.8215 (tp40) cc_final: 0.7721 (pm20) REVERT: B 190 MET cc_start: 0.8004 (tmm) cc_final: 0.7710 (tmm) REVERT: B 293 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8118 (p) REVERT: B 297 MET cc_start: 0.7911 (mtp) cc_final: 0.7676 (mtm) REVERT: B 313 LYS cc_start: 0.8987 (ttpt) cc_final: 0.8544 (tptt) REVERT: B 483 GLU cc_start: 0.7344 (tt0) cc_final: 0.7122 (tt0) REVERT: B 556 ASN cc_start: 0.8309 (t0) cc_final: 0.7810 (t0) REVERT: B 651 MET cc_start: 0.8752 (mmm) cc_final: 0.8422 (mmt) REVERT: B 736 GLN cc_start: 0.5095 (OUTLIER) cc_final: 0.4043 (tt0) REVERT: C 365 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7873 (mm-40) REVERT: C 583 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6127 (m-80) REVERT: D 102 GLN cc_start: 0.8217 (tp40) cc_final: 0.7722 (pm20) REVERT: D 190 MET cc_start: 0.8009 (tmm) cc_final: 0.7714 (tmm) REVERT: D 293 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8115 (p) REVERT: D 297 MET cc_start: 0.7918 (mtp) cc_final: 0.7681 (mtm) REVERT: D 313 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8545 (tptt) REVERT: D 483 GLU cc_start: 0.7341 (tt0) cc_final: 0.7119 (tt0) REVERT: D 556 ASN cc_start: 0.8307 (t0) cc_final: 0.7809 (t0) REVERT: D 651 MET cc_start: 0.8752 (mmm) cc_final: 0.8423 (mmt) REVERT: D 736 GLN cc_start: 0.5100 (OUTLIER) cc_final: 0.4050 (tt0) REVERT: F 409 GLN cc_start: 0.6295 (mp10) cc_final: 0.6070 (mt0) outliers start: 115 outliers final: 46 residues processed: 379 average time/residue: 1.0376 time to fit residues: 474.1479 Evaluate side-chains 291 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 237 time to evaluate : 2.621 ------------------------------------------------------------------------------- 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 577 SER 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 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 E residue 470 THR Chi-restraints excluded: chain E residue 500 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 492 ILE 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 577 SER 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 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 Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 276 optimal weight: 0.0030 chunk 298 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 274 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 228 HIS B 599 ASN E 487 ASN E 501 ASN C 435 ASN D 228 HIS D 599 ASN F 487 ASN F 501 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 26022 Z= 0.214 Angle : 0.659 9.099 35414 Z= 0.327 Chirality : 0.047 0.430 3980 Planarity : 0.004 0.048 4452 Dihedral : 7.489 59.505 4264 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.49 % Favored : 94.25 % Rotamer: Outliers : 3.73 % Allowed : 20.36 % Favored : 75.91 % 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: -2.33 (0.14), residues: 3060 helix: -1.04 (0.12), residues: 1710 sheet: -0.52 (0.46), residues: 118 loop : -2.29 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 436 HIS 0.021 0.002 HIS A 108 PHE 0.016 0.001 PHE D 746 TYR 0.020 0.001 TYR A 224 ARG 0.009 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 3 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 381 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 280 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.6175 (m-80) REVERT: B 26 LYS cc_start: 0.8089 (tttt) cc_final: 0.7823 (tmtt) REVERT: B 102 GLN cc_start: 0.8316 (tp40) cc_final: 0.7885 (pm20) REVERT: B 169 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7231 (ttm110) REVERT: B 190 MET cc_start: 0.7880 (tmm) cc_final: 0.7445 (tmm) REVERT: B 270 MET cc_start: 0.8711 (tpt) cc_final: 0.8497 (tpt) REVERT: B 293 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8332 (p) REVERT: B 297 MET cc_start: 0.7954 (mtp) cc_final: 0.7609 (mtm) REVERT: B 313 LYS cc_start: 0.9039 (ttpt) cc_final: 0.8609 (tptt) REVERT: B 335 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6836 (p0) REVERT: B 556 ASN cc_start: 0.8325 (t0) cc_final: 0.7799 (t0) REVERT: B 651 MET cc_start: 0.8760 (mmm) cc_final: 0.8502 (mmt) REVERT: B 736 GLN cc_start: 0.4347 (OUTLIER) cc_final: 0.3869 (tp40) REVERT: C 583 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: D 26 LYS cc_start: 0.8094 (tttt) cc_final: 0.7828 (tmtt) REVERT: D 102 GLN cc_start: 0.8317 (tp40) cc_final: 0.7886 (pm20) REVERT: D 169 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7231 (ttm110) REVERT: D 190 MET cc_start: 0.7882 (tmm) cc_final: 0.7448 (tmm) REVERT: D 270 MET cc_start: 0.8708 (tpt) cc_final: 0.8493 (tpt) REVERT: D 293 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8327 (p) REVERT: D 297 MET cc_start: 0.7962 (mtp) cc_final: 0.7617 (mtm) REVERT: D 313 LYS cc_start: 0.9039 (ttpt) cc_final: 0.8609 (tptt) REVERT: D 335 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6836 (p0) REVERT: D 556 ASN cc_start: 0.8322 (t0) cc_final: 0.7800 (t0) REVERT: D 651 MET cc_start: 0.8760 (mmm) cc_final: 0.8502 (mmt) REVERT: D 736 GLN cc_start: 0.4345 (OUTLIER) cc_final: 0.3869 (tp40) outliers start: 101 outliers final: 50 residues processed: 353 average time/residue: 1.2115 time to fit residues: 503.6005 Evaluate side-chains 284 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 224 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 440 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 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 763 THR 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 E residue 478 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 440 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 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.5980 chunk 207 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 263 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 531 GLN B 61 ASN B 228 HIS B 493 HIS B 599 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN C 8 ASN C 298 ASN C 531 GLN D 61 ASN D 228 HIS D 493 HIS D 599 ASN F 501 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26022 Z= 0.322 Angle : 0.714 10.972 35414 Z= 0.356 Chirality : 0.050 0.424 3980 Planarity : 0.005 0.052 4452 Dihedral : 7.082 59.932 4264 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 5.10 % Allowed : 20.47 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 3060 helix: -0.64 (0.12), residues: 1716 sheet: -0.08 (0.42), residues: 146 loop : -2.09 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 436 HIS 0.009 0.002 HIS B 228 PHE 0.015 0.001 PHE D 400 TYR 0.022 0.002 TYR A 578 ARG 0.007 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 4 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 404 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 266 time to evaluate : 2.607 Fit side-chains revert: symmetry clash REVERT: A 542 MET cc_start: 0.6653 (mtm) cc_final: 0.6424 (mtm) REVERT: A 583 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: A 588 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7497 (mm) REVERT: B 26 LYS cc_start: 0.7992 (tttt) cc_final: 0.7476 (mtpp) REVERT: B 102 GLN cc_start: 0.8346 (tp40) cc_final: 0.7923 (pm20) REVERT: B 140 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7274 (pp20) REVERT: B 169 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6691 (ttm110) REVERT: B 270 MET cc_start: 0.8609 (tpt) cc_final: 0.8363 (tpt) REVERT: B 297 MET cc_start: 0.7887 (mtp) cc_final: 0.7477 (mtm) REVERT: B 313 LYS cc_start: 0.9103 (ttpt) cc_final: 0.8683 (tptt) REVERT: B 556 ASN cc_start: 0.8386 (t0) cc_final: 0.7848 (t0) REVERT: B 579 MET cc_start: 0.8512 (ptt) cc_final: 0.8181 (ptt) REVERT: B 625 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8288 (mmmm) REVERT: B 678 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.4697 (ttt90) REVERT: B 706 MET cc_start: 0.8022 (ttp) cc_final: 0.7807 (ttt) REVERT: B 736 GLN cc_start: 0.4662 (OUTLIER) cc_final: 0.4225 (tp40) REVERT: E 365 TYR cc_start: 0.5611 (m-10) cc_final: 0.5349 (m-10) REVERT: C 542 MET cc_start: 0.6633 (mtm) cc_final: 0.6418 (mtm) REVERT: C 583 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: C 588 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7496 (mm) REVERT: D 26 LYS cc_start: 0.7988 (tttt) cc_final: 0.7473 (mtpp) REVERT: D 102 GLN cc_start: 0.8346 (tp40) cc_final: 0.7924 (pm20) REVERT: D 140 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7253 (pp20) REVERT: D 169 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6689 (ttm110) REVERT: D 270 MET cc_start: 0.8610 (tpt) cc_final: 0.8359 (tpt) REVERT: D 297 MET cc_start: 0.7902 (mtp) cc_final: 0.7493 (mtm) REVERT: D 313 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8683 (tptt) REVERT: D 556 ASN cc_start: 0.8382 (t0) cc_final: 0.7846 (t0) REVERT: D 579 MET cc_start: 0.8511 (ptt) cc_final: 0.8178 (ptt) REVERT: D 625 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8289 (mmmm) REVERT: D 678 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.4699 (ttt90) REVERT: D 706 MET cc_start: 0.8025 (ttp) cc_final: 0.7809 (ttt) REVERT: D 736 GLN cc_start: 0.4662 (OUTLIER) cc_final: 0.4225 (tp40) REVERT: F 365 TYR cc_start: 0.5620 (m-10) cc_final: 0.5357 (m-10) outliers start: 138 outliers final: 62 residues processed: 372 average time/residue: 1.0578 time to fit residues: 470.7713 Evaluate side-chains 296 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 220 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 LEU 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 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 763 THR 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 E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 LEU 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 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 625 LYS Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 744 ILE Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 7.9990 chunk 166 optimal weight: 0.0870 chunk 4 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 263 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 297 ASN A 435 ASN B 61 ASN B 228 HIS B 599 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN C 108 HIS C 297 ASN C 435 ASN D 61 ASN D 228 HIS D 599 ASN F 450 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 26022 Z= 0.203 Angle : 0.637 9.286 35414 Z= 0.315 Chirality : 0.046 0.401 3980 Planarity : 0.004 0.036 4452 Dihedral : 6.590 58.635 4260 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.36 % Favored : 94.38 % Rotamer: Outliers : 4.80 % Allowed : 21.69 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 3060 helix: -0.30 (0.13), residues: 1714 sheet: -0.51 (0.46), residues: 114 loop : -1.79 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 436 HIS 0.007 0.001 HIS D 228 PHE 0.012 0.001 PHE D 684 TYR 0.020 0.001 TYR A 578 ARG 0.008 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 5 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 389 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 259 time to evaluate : 2.768 Fit side-chains revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: A 583 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.6069 (m-80) REVERT: B 26 LYS cc_start: 0.8107 (tttt) cc_final: 0.7629 (mtpp) REVERT: B 102 GLN cc_start: 0.8322 (tp40) cc_final: 0.7939 (pm20) REVERT: B 270 MET cc_start: 0.8628 (tpt) cc_final: 0.8325 (tpt) REVERT: B 293 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8274 (p) REVERT: B 297 MET cc_start: 0.7882 (mtp) cc_final: 0.7650 (mtm) REVERT: B 313 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8668 (tptt) REVERT: B 345 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6974 (t-170) REVERT: B 556 ASN cc_start: 0.8362 (t0) cc_final: 0.7834 (t0) REVERT: B 579 MET cc_start: 0.8558 (ptt) cc_final: 0.8239 (ptt) REVERT: B 706 MET cc_start: 0.7921 (ttp) cc_final: 0.7586 (ttt) REVERT: B 736 GLN cc_start: 0.4461 (OUTLIER) cc_final: 0.4107 (tp40) REVERT: E 365 TYR cc_start: 0.5757 (m-10) cc_final: 0.5426 (m-10) REVERT: E 509 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6196 (mtt180) REVERT: C 179 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: C 583 TYR cc_start: 0.6536 (OUTLIER) cc_final: 0.6061 (m-80) REVERT: D 26 LYS cc_start: 0.8108 (tttt) cc_final: 0.7629 (mtpp) REVERT: D 102 GLN cc_start: 0.8321 (tp40) cc_final: 0.7937 (pm20) REVERT: D 270 MET cc_start: 0.8626 (tpt) cc_final: 0.8325 (tpt) REVERT: D 293 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8297 (p) REVERT: D 297 MET cc_start: 0.7888 (mtp) cc_final: 0.7655 (mtm) REVERT: D 313 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8667 (tptt) REVERT: D 345 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6973 (t-170) REVERT: D 556 ASN cc_start: 0.8357 (t0) cc_final: 0.7832 (t0) REVERT: D 579 MET cc_start: 0.8558 (ptt) cc_final: 0.8239 (ptt) REVERT: D 706 MET cc_start: 0.7923 (ttp) cc_final: 0.7587 (ttt) REVERT: D 736 GLN cc_start: 0.4460 (OUTLIER) cc_final: 0.4108 (tp40) REVERT: F 365 TYR cc_start: 0.5766 (m-10) cc_final: 0.5436 (m-10) REVERT: F 509 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.5731 (mtt180) outliers start: 130 outliers final: 53 residues processed: 362 average time/residue: 1.1972 time to fit residues: 518.8677 Evaluate side-chains 293 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 228 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 LEU 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 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 763 THR 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 E residue 478 THR Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 LEU 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 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 509 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.7980 chunk 264 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 294 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 24 optimal weight: 0.0270 chunk 97 optimal weight: 4.9990 chunk 154 optimal weight: 0.0270 overall best weight: 1.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 297 ASN A 435 ASN B 61 ASN B 599 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN E 501 ASN C 297 ASN C 435 ASN D 61 ASN D 599 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26022 Z= 0.210 Angle : 0.629 9.254 35414 Z= 0.311 Chirality : 0.046 0.397 3980 Planarity : 0.004 0.036 4452 Dihedral : 6.326 58.288 4260 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.46 % Favored : 94.28 % Rotamer: Outliers : 4.40 % Allowed : 22.73 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3060 helix: 0.00 (0.13), residues: 1694 sheet: -0.53 (0.46), residues: 114 loop : -1.68 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 436 HIS 0.013 0.001 HIS A 108 PHE 0.012 0.001 PHE B 684 TYR 0.020 0.001 TYR A 578 ARG 0.008 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 6 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 352 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 233 time to evaluate : 2.811 Fit side-chains revert: symmetry clash REVERT: A 583 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.6116 (m-80) REVERT: B 26 LYS cc_start: 0.8029 (tttt) cc_final: 0.7633 (mtpp) REVERT: B 102 GLN cc_start: 0.8315 (tp40) cc_final: 0.7955 (pm20) REVERT: B 293 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8082 (p) REVERT: B 297 MET cc_start: 0.7882 (mtp) cc_final: 0.7411 (mtm) REVERT: B 313 LYS cc_start: 0.9123 (ttpt) cc_final: 0.8679 (tptt) REVERT: B 335 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6725 (p0) REVERT: B 345 HIS cc_start: 0.7237 (t-90) cc_final: 0.6815 (m170) REVERT: B 556 ASN cc_start: 0.8451 (t0) cc_final: 0.7894 (t0) REVERT: B 636 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8165 (p0) REVERT: B 678 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.4706 (ttt90) REVERT: B 706 MET cc_start: 0.7897 (ttp) cc_final: 0.7545 (ttt) REVERT: E 365 TYR cc_start: 0.5723 (m-10) cc_final: 0.5381 (m-10) REVERT: E 509 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.5893 (mtt180) REVERT: C 583 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.6074 (m-80) REVERT: D 26 LYS cc_start: 0.8030 (tttt) cc_final: 0.7634 (mtpp) REVERT: D 102 GLN cc_start: 0.8314 (tp40) cc_final: 0.7952 (pm20) REVERT: D 293 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8108 (p) REVERT: D 297 MET cc_start: 0.7890 (mtp) cc_final: 0.7416 (mtm) REVERT: D 313 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8677 (tptt) REVERT: D 335 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6725 (p0) REVERT: D 345 HIS cc_start: 0.7232 (t-90) cc_final: 0.6814 (m170) REVERT: D 556 ASN cc_start: 0.8450 (t0) cc_final: 0.7894 (t0) REVERT: D 636 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8162 (p0) REVERT: D 678 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.4681 (ttt90) REVERT: D 706 MET cc_start: 0.7900 (ttp) cc_final: 0.7548 (ttt) REVERT: F 365 TYR cc_start: 0.5734 (m-10) cc_final: 0.5394 (m-10) REVERT: F 509 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6658 (ptt180) outliers start: 119 outliers final: 58 residues processed: 332 average time/residue: 1.1377 time to fit residues: 448.4569 Evaluate side-chains 289 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 219 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 763 THR 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 E residue 478 THR Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 636 ASN Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 509 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.0070 chunk 33 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 293 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 135 optimal weight: 30.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 130 ASN A 297 ASN A 435 ASN B 599 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN C 108 HIS C 297 ASN C 435 ASN D 599 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 26022 Z= 0.155 Angle : 0.615 9.497 35414 Z= 0.302 Chirality : 0.045 0.408 3980 Planarity : 0.004 0.037 4452 Dihedral : 5.946 58.228 4254 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.33 % Favored : 94.41 % Rotamer: Outliers : 3.70 % Allowed : 24.24 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3060 helix: 0.16 (0.13), residues: 1714 sheet: -0.50 (0.46), residues: 114 loop : -1.58 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 436 HIS 0.005 0.001 HIS B 34 PHE 0.012 0.001 PHE A 550 TYR 0.026 0.001 TYR A 578 ARG 0.008 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 7 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 334 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 234 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.5790 (m-10) REVERT: B 26 LYS cc_start: 0.8026 (tttt) cc_final: 0.7650 (mtpp) REVERT: B 102 GLN cc_start: 0.8342 (tp40) cc_final: 0.7983 (pm20) REVERT: B 148 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6936 (mp) REVERT: B 293 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8291 (p) REVERT: B 345 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6644 (m170) REVERT: B 556 ASN cc_start: 0.8436 (t0) cc_final: 0.7902 (t0) REVERT: B 678 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.4717 (ttt90) REVERT: E 365 TYR cc_start: 0.5718 (m-10) cc_final: 0.5432 (m-10) REVERT: E 464 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.5302 (m-80) REVERT: C 583 TYR cc_start: 0.6275 (OUTLIER) cc_final: 0.5803 (m-10) REVERT: D 26 LYS cc_start: 0.8027 (tttt) cc_final: 0.7651 (mtpp) REVERT: D 102 GLN cc_start: 0.8343 (tp40) cc_final: 0.7983 (pm20) REVERT: D 148 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6933 (mp) REVERT: D 293 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8286 (p) REVERT: D 345 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6648 (m170) REVERT: D 556 ASN cc_start: 0.8434 (t0) cc_final: 0.7899 (t0) REVERT: D 678 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.4717 (ttt90) REVERT: F 365 TYR cc_start: 0.5733 (m-10) cc_final: 0.5438 (m-10) REVERT: F 464 PHE cc_start: 0.5575 (OUTLIER) cc_final: 0.5293 (m-80) outliers start: 100 outliers final: 60 residues processed: 314 average time/residue: 1.0917 time to fit residues: 411.1335 Evaluate side-chains 286 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 214 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU 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 E residue 464 PHE Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 501 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 435 ASN B 61 ASN B 599 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN C 297 ASN C 435 ASN D 61 ASN D 599 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26022 Z= 0.300 Angle : 0.673 9.846 35414 Z= 0.332 Chirality : 0.048 0.392 3980 Planarity : 0.004 0.043 4452 Dihedral : 6.037 57.377 4254 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.65 % Favored : 94.08 % Rotamer: Outliers : 3.70 % Allowed : 24.39 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 3060 helix: 0.14 (0.13), residues: 1720 sheet: -0.54 (0.46), residues: 114 loop : -1.52 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 436 HIS 0.005 0.001 HIS B 34 PHE 0.023 0.001 PHE A 503 TYR 0.022 0.002 TYR C 578 ARG 0.008 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 8 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 321 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 221 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 TYR cc_start: 0.6464 (OUTLIER) cc_final: 0.6089 (m-10) REVERT: B 26 LYS cc_start: 0.8101 (tttt) cc_final: 0.7686 (mtpp) REVERT: B 102 GLN cc_start: 0.8381 (tp40) cc_final: 0.8013 (pm20) REVERT: B 270 MET cc_start: 0.8742 (tpt) cc_final: 0.8449 (tpt) REVERT: B 345 HIS cc_start: 0.7263 (t-90) cc_final: 0.6881 (m170) REVERT: B 556 ASN cc_start: 0.8490 (t0) cc_final: 0.7955 (t0) REVERT: B 678 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.4584 (ttt90) REVERT: B 706 MET cc_start: 0.7933 (ttp) cc_final: 0.7649 (ttt) REVERT: E 365 TYR cc_start: 0.5942 (m-10) cc_final: 0.5680 (m-10) REVERT: C 583 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.6079 (m-10) REVERT: D 26 LYS cc_start: 0.8103 (tttt) cc_final: 0.7687 (mtpp) REVERT: D 102 GLN cc_start: 0.8381 (tp40) cc_final: 0.8012 (pm20) REVERT: D 270 MET cc_start: 0.8740 (tpt) cc_final: 0.8447 (tpt) REVERT: D 345 HIS cc_start: 0.7261 (t-90) cc_final: 0.6883 (m170) REVERT: D 556 ASN cc_start: 0.8487 (t0) cc_final: 0.7952 (t0) REVERT: D 678 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.4582 (ttt90) REVERT: D 706 MET cc_start: 0.7933 (ttp) cc_final: 0.7648 (ttt) outliers start: 100 outliers final: 71 residues processed: 303 average time/residue: 1.0086 time to fit residues: 369.1974 Evaluate side-chains 279 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 204 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 763 THR 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 E residue 489 TYR Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 501 ASN Chi-restraints excluded: chain F residue 514 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.8980 chunk 280 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 chunk 273 optimal weight: 0.0050 chunk 164 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 246 optimal weight: 0.3980 chunk 258 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 435 ASN B 599 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN C 297 ASN C 435 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 26022 Z= 0.158 Angle : 0.621 9.503 35414 Z= 0.306 Chirality : 0.045 0.383 3980 Planarity : 0.004 0.041 4452 Dihedral : 5.779 58.029 4254 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.93 % Favored : 94.80 % Rotamer: Outliers : 2.85 % Allowed : 25.13 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 3060 helix: 0.28 (0.13), residues: 1730 sheet: -0.49 (0.46), residues: 114 loop : -1.48 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 436 HIS 0.006 0.001 HIS B 34 PHE 0.027 0.001 PHE C 503 TYR 0.021 0.001 TYR A 87 ARG 0.009 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 9 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 298 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 221 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8085 (tttt) cc_final: 0.7696 (mtpp) REVERT: B 83 TYR cc_start: 0.7415 (m-80) cc_final: 0.7187 (m-80) REVERT: B 102 GLN cc_start: 0.8368 (tp40) cc_final: 0.8037 (pm20) REVERT: B 148 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6944 (mp) REVERT: B 270 MET cc_start: 0.8693 (tpt) cc_final: 0.8458 (tpt) REVERT: B 345 HIS cc_start: 0.7093 (t-90) cc_final: 0.6791 (m170) REVERT: B 556 ASN cc_start: 0.8461 (t0) cc_final: 0.7996 (t0) REVERT: B 678 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.4808 (ttt90) REVERT: B 706 MET cc_start: 0.7782 (ttp) cc_final: 0.7503 (ttt) REVERT: B 713 ASP cc_start: 0.8346 (m-30) cc_final: 0.8034 (m-30) REVERT: E 365 TYR cc_start: 0.6030 (m-10) cc_final: 0.5710 (m-10) REVERT: E 464 PHE cc_start: 0.5793 (OUTLIER) cc_final: 0.5419 (m-80) REVERT: D 83 TYR cc_start: 0.7413 (m-80) cc_final: 0.7186 (m-80) REVERT: D 102 GLN cc_start: 0.8369 (tp40) cc_final: 0.8036 (pm20) REVERT: D 148 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6941 (mp) REVERT: D 270 MET cc_start: 0.8690 (tpt) cc_final: 0.8458 (tpt) REVERT: D 345 HIS cc_start: 0.7097 (t-90) cc_final: 0.6800 (m170) REVERT: D 556 ASN cc_start: 0.8460 (t0) cc_final: 0.7996 (t0) REVERT: D 678 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.4801 (ttt90) REVERT: D 706 MET cc_start: 0.7785 (ttp) cc_final: 0.7505 (ttt) REVERT: D 713 ASP cc_start: 0.8351 (m-30) cc_final: 0.8039 (m-30) REVERT: F 464 PHE cc_start: 0.5779 (OUTLIER) cc_final: 0.5411 (m-80) outliers start: 77 outliers final: 55 residues processed: 284 average time/residue: 1.0613 time to fit residues: 364.2119 Evaluate side-chains 265 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 204 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 744 ILE 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 E residue 464 PHE Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 744 ILE Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.0980 chunk 288 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 302 optimal weight: 8.9990 chunk 278 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 435 ASN B 599 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN C 297 ASN C 435 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26022 Z= 0.158 Angle : 0.618 11.530 35414 Z= 0.304 Chirality : 0.045 0.384 3980 Planarity : 0.004 0.049 4452 Dihedral : 5.586 57.598 4254 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.26 % Favored : 94.48 % Rotamer: Outliers : 2.73 % Allowed : 25.13 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 3060 helix: 0.37 (0.13), residues: 1730 sheet: -0.41 (0.47), residues: 114 loop : -1.41 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 436 HIS 0.006 0.001 HIS D 34 PHE 0.031 0.001 PHE D 72 TYR 0.018 0.001 TYR C 488 ARG 0.010 0.000 ARG D 306 ********************** REFINEMENT MACRO_CYCLE 10 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 283 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 209 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 GLN cc_start: 0.8359 (tp40) cc_final: 0.8053 (pm20) REVERT: B 148 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6922 (mp) REVERT: B 345 HIS cc_start: 0.7046 (t-90) cc_final: 0.6780 (m170) REVERT: B 556 ASN cc_start: 0.8494 (t0) cc_final: 0.8049 (t0) REVERT: B 625 LYS cc_start: 0.8587 (tppp) cc_final: 0.8295 (mmmm) REVERT: B 678 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.4744 (ttt90) REVERT: B 706 MET cc_start: 0.7682 (ttp) cc_final: 0.7354 (ttt) REVERT: B 713 ASP cc_start: 0.8271 (m-30) cc_final: 0.7967 (m-30) REVERT: E 365 TYR cc_start: 0.6028 (m-10) cc_final: 0.5777 (m-10) REVERT: E 464 PHE cc_start: 0.5848 (OUTLIER) cc_final: 0.5432 (m-80) REVERT: D 102 GLN cc_start: 0.8362 (tp40) cc_final: 0.8053 (pm20) REVERT: D 148 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6925 (mp) REVERT: D 345 HIS cc_start: 0.7050 (t-90) cc_final: 0.6795 (m170) REVERT: D 556 ASN cc_start: 0.8493 (t0) cc_final: 0.8047 (t0) REVERT: D 625 LYS cc_start: 0.8587 (tppp) cc_final: 0.8299 (mmmm) REVERT: D 678 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.4740 (ttt90) REVERT: D 706 MET cc_start: 0.7685 (ttp) cc_final: 0.7358 (ttt) REVERT: D 713 ASP cc_start: 0.8276 (m-30) cc_final: 0.7972 (m-30) REVERT: F 464 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.5438 (m-80) outliers start: 74 outliers final: 53 residues processed: 274 average time/residue: 1.0543 time to fit residues: 346.4131 Evaluate side-chains 259 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 200 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 744 ILE 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 E residue 464 PHE Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 744 ILE Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 501 ASN Chi-restraints excluded: chain F residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 ASN C 297 ASN C 435 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.158380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.105324 restraints weight = 44638.593| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.99 r_work: 0.3176 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26022 Z= 0.252 Angle : 0.658 12.309 35414 Z= 0.325 Chirality : 0.047 0.387 3980 Planarity : 0.004 0.054 4452 Dihedral : 5.665 57.328 4254 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.36 % Favored : 94.38 % Rotamer: Outliers : 2.51 % Allowed : 25.42 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 3060 helix: 0.34 (0.13), residues: 1716 sheet: -0.36 (0.47), residues: 114 loop : -1.40 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 436 HIS 0.007 0.001 HIS B 34 PHE 0.022 0.001 PHE C 503 TYR 0.019 0.002 TYR C 488 ARG 0.012 0.001 ARG D 306 =============================================================================== Job complete usr+sys time: 8592.22 seconds wall clock time: 153 minutes 54.99 seconds (9234.99 seconds total)