Starting phenix.real_space_refine on Mon Feb 19 15:54:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y76_33653/02_2024/7y76_33653_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y76_33653/02_2024/7y76_33653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y76_33653/02_2024/7y76_33653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y76_33653/02_2024/7y76_33653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y76_33653/02_2024/7y76_33653_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y76_33653/02_2024/7y76_33653_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 S 146 5.16 5 C 16340 2.51 5 N 4006 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C GLU 430": "OE1" <-> "OE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ARG 518": "NH1" <-> "NH2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C GLU 564": "OE1" <-> "OE2" Residue "C GLU 639": "OE1" <-> "OE2" Residue "C ARG 671": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "C GLU 699": "OE1" <-> "OE2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F GLU 465": "OE1" <-> "OE2" Residue "F GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25180 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4499 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 552} Chain: "A" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6102 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1578 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4499 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 552} Chain: "C" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6102 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain: "F" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1578 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PH': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PH': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.50, per 1000 atoms: 0.58 Number of scatterers: 25180 At special positions: 0 Unit cell: (159.789, 144.571, 216.313, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 146 16.00 P 6 15.00 O 4680 8.00 N 4006 7.00 C 16340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.05 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.04 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 901 " - " ASN A 322 " " NAG B1001 " - " ASN B 131 " " NAG B1002 " - " ASN B 332 " " NAG C 901 " - " ASN C 322 " " NAG D1001 " - " ASN D 131 " " NAG D1002 " - " ASN D 332 " " NAG G 1 " - " ASN B 357 " " NAG H 1 " - " ASN A 53 " " NAG I 1 " - " ASN A 90 " " NAG J 1 " - " ASN A 103 " " NAG K 1 " - " ASN A 432 " " NAG L 1 " - " ASN A 546 " " NAG M 1 " - " ASN A 690 " " NAG N 1 " - " ASN E 343 " " NAG O 1 " - " ASN D 357 " " NAG P 1 " - " ASN C 53 " " NAG Q 1 " - " ASN C 90 " " NAG R 1 " - " ASN C 103 " " NAG S 1 " - " ASN C 432 " " NAG T 1 " - " ASN C 546 " " NAG U 1 " - " ASN C 690 " " NAG V 1 " - " ASN F 343 " Time building additional restraints: 10.80 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 378 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 374 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 378 " 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 134 helices and 8 sheets defined 54.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 Processing helix chain 'B' and resid 30 through 38 removed outlier: 3.823A pdb=" N TYR B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 54 removed outlier: 3.848A pdb=" N VAL B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 56 through 69 Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 86 through 116 removed outlier: 3.969A pdb=" N MET B 100 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 116 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 137 through 141 removed outlier: 3.984A pdb=" N LYS B 141 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 169 through 186 Processing helix chain 'B' and resid 196 through 215 Proline residue: B 203 - end of helix Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.648A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 272 through 320 removed outlier: 3.909A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 339 Processing helix chain 'B' and resid 345 through 354 removed outlier: 4.963A pdb=" N GLU B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Proline residue: B 353 - end of helix Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 373 through 382 Processing helix chain 'B' and resid 389 through 419 removed outlier: 3.774A pdb=" N ALA B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Proline residue: B 417 - end of helix Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 430 through 449 removed outlier: 5.229A pdb=" N VAL B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 482 removed outlier: 4.152A pdb=" N ASP B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 497 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 527 removed outlier: 3.677A pdb=" N VAL B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 567 removed outlier: 4.172A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'A' and resid 22 through 52 removed outlier: 3.517A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 80 Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.566A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.784A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.668A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 194 removed outlier: 3.614A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.768A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 removed outlier: 4.745A pdb=" N ASP A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.577A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.880A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 279 through 282 No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.647A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.797A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.966A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.943A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 3.708A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 465 removed outlier: 3.985A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 473 through 483 removed outlier: 3.635A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 504 through 507 No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 513 through 532 removed outlier: 4.389A pdb=" N THR A 517 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 521 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 522 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 525 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 529 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.874A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 573 removed outlier: 3.761A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'A' and resid 624 through 628 Processing helix chain 'A' and resid 637 through 657 Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.722A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 766 Processing helix chain 'E' and resid 338 through 341 No H-bonds generated for 'chain 'E' and resid 338 through 341' Processing helix chain 'E' and resid 404 through 409 removed outlier: 4.519A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 421 Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'D' and resid 12 through 22 Processing helix chain 'D' and resid 30 through 38 removed outlier: 3.823A pdb=" N TYR D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 54 removed outlier: 3.848A pdb=" N VAL D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 56 through 69 Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 86 through 116 removed outlier: 3.968A pdb=" N MET D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 116 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 137 through 141 removed outlier: 3.985A pdb=" N LYS D 141 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 169 through 186 Processing helix chain 'D' and resid 196 through 215 Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 220 through 228 removed outlier: 3.649A pdb=" N LEU D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 272 through 320 removed outlier: 3.909A pdb=" N ILE D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 339 Processing helix chain 'D' and resid 345 through 354 removed outlier: 4.963A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Proline residue: D 353 - end of helix Processing helix chain 'D' and resid 360 through 365 Processing helix chain 'D' and resid 373 through 382 Processing helix chain 'D' and resid 389 through 419 removed outlier: 3.774A pdb=" N ALA D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Proline residue: D 417 - end of helix Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 430 through 449 removed outlier: 5.229A pdb=" N VAL D 447 " --> pdb=" O ALA D 443 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR D 449 " --> pdb=" O GLY D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 482 removed outlier: 4.151A pdb=" N ASP D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 497 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 527 removed outlier: 3.679A pdb=" N VAL D 518 " --> pdb=" O PRO D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 567 removed outlier: 4.171A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 581 Processing helix chain 'C' and resid 22 through 52 removed outlier: 3.517A pdb=" N GLU C 37 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 80 Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 110 through 129 removed outlier: 3.566A pdb=" N ASN C 121 " --> pdb=" O ASN C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 154 removed outlier: 3.783A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 removed outlier: 3.668A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 194 removed outlier: 3.614A pdb=" N ARG C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.768A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 206 removed outlier: 4.746A pdb=" N ASP C 206 " --> pdb=" O TYR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.578A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 248 removed outlier: 3.880A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 279 through 282 No H-bonds generated for 'chain 'C' and resid 279 through 282' Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.647A pdb=" N VAL C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 318 removed outlier: 3.797A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 330 No H-bonds generated for 'chain 'C' and resid 327 through 330' Processing helix chain 'C' and resid 367 through 382 removed outlier: 3.966A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 387 No H-bonds generated for 'chain 'C' and resid 385 through 387' Processing helix chain 'C' and resid 390 through 392 No H-bonds generated for 'chain 'C' and resid 390 through 392' Processing helix chain 'C' and resid 400 through 413 removed outlier: 3.942A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 removed outlier: 3.709A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 465 removed outlier: 3.984A pdb=" N ILE C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 449 " --> pdb=" O THR C 445 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 450 " --> pdb=" O ILE C 446 " (cutoff:3.500A) Proline residue: C 451 - end of helix Processing helix chain 'C' and resid 473 through 483 removed outlier: 3.635A pdb=" N ARG C 482 " --> pdb=" O TRP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 502 No H-bonds generated for 'chain 'C' and resid 500 through 502' Processing helix chain 'C' and resid 504 through 507 No H-bonds generated for 'chain 'C' and resid 504 through 507' Processing helix chain 'C' and resid 513 through 532 removed outlier: 4.389A pdb=" N THR C 517 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR C 521 " --> pdb=" O ARG C 518 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN C 522 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE C 525 " --> pdb=" O GLN C 522 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU C 529 " --> pdb=" O GLN C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 541 No H-bonds generated for 'chain 'C' and resid 539 through 541' Processing helix chain 'C' and resid 548 through 560 removed outlier: 3.874A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 573 removed outlier: 3.762A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 587 Processing helix chain 'C' and resid 589 through 598 Processing helix chain 'C' and resid 624 through 628 Processing helix chain 'C' and resid 637 through 657 Processing helix chain 'C' and resid 697 through 715 removed outlier: 3.722A pdb=" N SER C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 766 Processing helix chain 'F' and resid 338 through 341 No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 404 through 409 removed outlier: 4.518A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing sheet with id= A, first strand: chain 'A' and resid 131 through 133 Processing sheet with id= B, first strand: chain 'A' and resid 347 through 349 Processing sheet with id= C, first strand: chain 'A' and resid 722 through 725 removed outlier: 4.648A pdb=" N LYS A 619 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.634A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 131 through 133 Processing sheet with id= F, first strand: chain 'C' and resid 347 through 349 Processing sheet with id= G, first strand: chain 'C' and resid 722 through 725 removed outlier: 4.648A pdb=" N LYS C 619 " --> pdb=" O LEU C 725 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.636A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3000 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: 8.20 Time building geometry restraints manager: 11.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7742 1.34 - 1.47: 6946 1.47 - 1.60: 10912 1.60 - 1.72: 6 1.72 - 1.85: 232 Bond restraints: 25838 Sorted by residual: bond pdb=" C31 3PH D1003 " pdb=" O31 3PH D1003 " ideal model delta sigma weight residual 1.325 1.456 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C31 3PH B1003 " pdb=" O31 3PH B1003 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C31 3PH D1005 " pdb=" O31 3PH D1005 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C21 3PH D1003 " pdb=" O21 3PH D1003 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C21 3PH B1003 " pdb=" O21 3PH B1003 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 25833 not shown) Histogram of bond angle deviations from ideal: 98.91 - 106.85: 802 106.85 - 114.79: 15362 114.79 - 122.73: 17081 122.73 - 130.67: 1695 130.67 - 138.61: 128 Bond angle restraints: 35068 Sorted by residual: angle pdb=" N VAL E 367 " pdb=" CA VAL E 367 " pdb=" C VAL E 367 " ideal model delta sigma weight residual 113.71 107.40 6.31 9.50e-01 1.11e+00 4.41e+01 angle pdb=" N VAL F 367 " pdb=" CA VAL F 367 " pdb=" C VAL F 367 " ideal model delta sigma weight residual 113.71 107.44 6.27 9.50e-01 1.11e+00 4.36e+01 angle pdb=" C LEU A 267 " pdb=" N GLY A 268 " pdb=" CA GLY A 268 " ideal model delta sigma weight residual 123.30 117.60 5.70 1.06e+00 8.90e-01 2.89e+01 angle pdb=" C LEU C 267 " pdb=" N GLY C 268 " pdb=" CA GLY C 268 " ideal model delta sigma weight residual 123.30 117.61 5.69 1.06e+00 8.90e-01 2.88e+01 angle pdb=" N PRO E 373 " pdb=" CA PRO E 373 " pdb=" C PRO E 373 " ideal model delta sigma weight residual 113.47 106.03 7.44 1.43e+00 4.89e-01 2.71e+01 ... (remaining 35063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 13521 17.14 - 34.27: 1613 34.27 - 51.41: 473 51.41 - 68.55: 119 68.55 - 85.68: 26 Dihedral angle restraints: 15752 sinusoidal: 6848 harmonic: 8904 Sorted by residual: dihedral pdb=" CB CYS F 379 " pdb=" SG CYS F 379 " pdb=" SG CYS F 432 " pdb=" CB CYS F 432 " ideal model delta sinusoidal sigma weight residual 93.00 40.25 52.75 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 40.28 52.72 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 48.73 44.27 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 15749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3554 0.085 - 0.169: 318 0.169 - 0.254: 24 0.254 - 0.338: 4 0.338 - 0.423: 2 Chirality restraints: 3902 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 90 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA PHE E 374 " pdb=" N PHE E 374 " pdb=" C PHE E 374 " pdb=" CB PHE E 374 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3899 not shown) Planarity restraints: 4390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 687 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 688 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 688 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 688 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 687 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO C 688 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 688 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 688 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 234 " 0.028 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO C 235 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " 0.023 5.00e-02 4.00e+02 ... (remaining 4387 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 291 2.58 - 3.16: 22338 3.16 - 3.74: 38118 3.74 - 4.32: 52235 4.32 - 4.90: 86244 Nonbonded interactions: 199226 Sorted by model distance: nonbonded pdb=" OE1 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.996 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.996 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 2.087 2.230 nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 2.089 2.230 nonbonded pdb=" O ASN E 439 " pdb=" OG SER E 443 " model vdw 2.203 2.440 ... (remaining 199221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.180 Check model and map are aligned: 0.350 Set scattering table: 0.240 Process input model: 74.600 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.340 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.010 0.131 25838 Z= 0.616 Angle : 0.844 13.613 35068 Z= 0.443 Chirality : 0.052 0.423 3902 Planarity : 0.004 0.049 4368 Dihedral : 16.482 85.684 10000 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.84 % Favored : 90.83 % Rotamer: Outliers : 5.15 % Allowed : 16.06 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.13), residues: 3030 helix: -1.66 (0.11), residues: 1662 sheet: -1.29 (0.45), residues: 116 loop : -3.15 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 459 HIS 0.007 0.001 HIS A 241 PHE 0.019 0.002 PHE B 295 TYR 0.025 0.002 TYR C 183 ARG 0.003 0.000 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 209 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 225 MET cc_start: 0.7887 (mtt) cc_final: 0.7587 (mtt) REVERT: A 323 MET cc_start: 0.8921 (mmp) cc_final: 0.8693 (mmp) REVERT: A 736 GLN cc_start: 0.3725 (OUTLIER) cc_final: 0.3177 (tm-30) REVERT: E 357 ARG cc_start: 0.7917 (tmm-80) cc_final: 0.7634 (tmm-80) REVERT: E 471 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 472 ILE cc_start: 0.8965 (mm) cc_final: 0.8743 (mt) REVERT: D 77 TRP cc_start: 0.6830 (m100) cc_final: 0.6123 (m100) REVERT: D 225 MET cc_start: 0.7890 (mtt) cc_final: 0.7592 (mtt) REVERT: C 406 GLU cc_start: 0.8022 (tp30) cc_final: 0.7803 (mm-30) REVERT: C 736 GLN cc_start: 0.3573 (OUTLIER) cc_final: 0.3315 (tt0) REVERT: F 472 ILE cc_start: 0.9021 (mm) cc_final: 0.8805 (mt) outliers start: 136 outliers final: 82 residues processed: 330 average time/residue: 0.3334 time to fit residues: 179.7297 Evaluate side-chains 255 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 171 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 chunk 127 optimal weight: 0.3980 chunk 78 optimal weight: 0.1980 chunk 154 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 274 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN B 243 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 461 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 GLN A 96 GLN A 159 ASN A 210 ASN A 239 HIS A 378 HIS A 472 GLN A 493 HIS A 505 HIS A 599 ASN E 422 ASN D 167 GLN D 243 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN D 461 ASN ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 96 GLN C 102 GLN C 159 ASN C 210 ASN C 239 HIS C 378 HIS C 472 GLN C 493 HIS C 505 HIS C 599 ASN F 422 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25838 Z= 0.160 Angle : 0.605 9.119 35068 Z= 0.298 Chirality : 0.042 0.283 3902 Planarity : 0.004 0.056 4368 Dihedral : 11.224 77.558 4486 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.34 % Favored : 93.50 % Rotamer: Outliers : 3.37 % Allowed : 18.60 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.15), residues: 3030 helix: -0.13 (0.13), residues: 1674 sheet: -1.03 (0.53), residues: 92 loop : -2.57 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 77 HIS 0.006 0.001 HIS A 34 PHE 0.017 0.001 PHE F 374 TYR 0.027 0.001 TYR D 504 ARG 0.005 0.000 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 201 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 MET cc_start: 0.8081 (mmm) cc_final: 0.7532 (mpp) REVERT: B 225 MET cc_start: 0.8063 (mtt) cc_final: 0.7842 (mtt) REVERT: B 384 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7571 (t0) REVERT: B 446 MET cc_start: 0.7768 (tpp) cc_final: 0.7391 (tpp) REVERT: B 503 TRP cc_start: 0.4925 (m100) cc_final: 0.3946 (t-100) REVERT: A 123 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: E 458 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8622 (mmmt) REVERT: E 472 ILE cc_start: 0.9083 (mm) cc_final: 0.8778 (mt) REVERT: D 100 MET cc_start: 0.8531 (mtt) cc_final: 0.7772 (mpp) REVERT: D 225 MET cc_start: 0.8018 (mtt) cc_final: 0.7788 (mtt) REVERT: D 450 MET cc_start: 0.8590 (tpp) cc_final: 0.8061 (tpp) REVERT: C 102 GLN cc_start: 0.8663 (pt0) cc_final: 0.8278 (pm20) REVERT: F 458 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8569 (mmmt) REVERT: F 465 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8032 (tm-30) REVERT: F 472 ILE cc_start: 0.9214 (mm) cc_final: 0.9000 (mt) outliers start: 89 outliers final: 44 residues processed: 280 average time/residue: 0.3296 time to fit residues: 152.2374 Evaluate side-chains 227 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 181 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 244 optimal weight: 0.1980 chunk 272 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 220 optimal weight: 0.0670 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN B 275 HIS ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25838 Z= 0.191 Angle : 0.584 9.413 35068 Z= 0.287 Chirality : 0.042 0.277 3902 Planarity : 0.003 0.043 4368 Dihedral : 9.957 77.048 4410 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.23 % Favored : 92.61 % Rotamer: Outliers : 3.37 % Allowed : 19.13 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3030 helix: 0.30 (0.13), residues: 1684 sheet: -0.74 (0.53), residues: 92 loop : -2.35 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 505 HIS 0.004 0.001 HIS A 34 PHE 0.016 0.001 PHE C 315 TYR 0.037 0.001 TYR B 504 ARG 0.004 0.000 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 189 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.8301 (mtt) cc_final: 0.7733 (mpp) REVERT: B 225 MET cc_start: 0.8095 (mtt) cc_final: 0.7877 (mtt) REVERT: B 446 MET cc_start: 0.7809 (tpp) cc_final: 0.7442 (tpp) REVERT: B 450 MET cc_start: 0.8681 (tpp) cc_final: 0.8361 (tpp) REVERT: A 123 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8559 (mtm) REVERT: E 458 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8595 (mmmt) REVERT: D 225 MET cc_start: 0.8065 (mtt) cc_final: 0.7840 (mtt) REVERT: F 357 ARG cc_start: 0.7133 (tmm-80) cc_final: 0.6932 (tmm-80) REVERT: F 458 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8514 (mmmt) outliers start: 89 outliers final: 51 residues processed: 260 average time/residue: 0.3199 time to fit residues: 138.1441 Evaluate side-chains 221 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 169 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 384 ASN Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 275 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 243 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN A 345 HIS E 417 ASN D 13 GLN D 243 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25838 Z= 0.286 Angle : 0.598 10.377 35068 Z= 0.292 Chirality : 0.043 0.272 3902 Planarity : 0.003 0.041 4368 Dihedral : 9.455 75.901 4403 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.33 % Favored : 92.51 % Rotamer: Outliers : 3.48 % Allowed : 19.92 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3030 helix: 0.41 (0.13), residues: 1708 sheet: -0.69 (0.54), residues: 90 loop : -2.21 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 505 HIS 0.005 0.001 HIS A 241 PHE 0.020 0.001 PHE D 489 TYR 0.020 0.001 TYR A 183 ARG 0.002 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 181 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.5145 (OUTLIER) cc_final: 0.4540 (m-10) REVERT: B 225 MET cc_start: 0.8073 (mtt) cc_final: 0.7849 (mtt) REVERT: B 446 MET cc_start: 0.7788 (tpp) cc_final: 0.7454 (tpp) REVERT: A 123 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8554 (mtm) REVERT: A 256 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9321 (mm) REVERT: D 83 TYR cc_start: 0.4792 (OUTLIER) cc_final: 0.4189 (m-10) REVERT: D 225 MET cc_start: 0.8067 (mtt) cc_final: 0.7843 (mtt) REVERT: D 385 MET cc_start: 0.8419 (mmm) cc_final: 0.7135 (mtt) REVERT: D 450 MET cc_start: 0.8532 (tpp) cc_final: 0.8218 (tpp) REVERT: C 736 GLN cc_start: 0.3394 (OUTLIER) cc_final: 0.2726 (tm-30) outliers start: 92 outliers final: 52 residues processed: 260 average time/residue: 0.3205 time to fit residues: 140.8725 Evaluate side-chains 219 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 162 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 149 optimal weight: 9.9990 chunk 262 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 243 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 25838 Z= 0.149 Angle : 0.561 9.469 35068 Z= 0.272 Chirality : 0.041 0.277 3902 Planarity : 0.003 0.038 4368 Dihedral : 8.897 74.803 4395 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.70 % Favored : 93.20 % Rotamer: Outliers : 3.11 % Allowed : 20.42 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3030 helix: 0.53 (0.13), residues: 1722 sheet: -0.32 (0.54), residues: 88 loop : -2.03 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 77 HIS 0.004 0.001 HIS C 34 PHE 0.012 0.001 PHE C 315 TYR 0.016 0.001 TYR F 396 ARG 0.008 0.000 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 189 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4939 (OUTLIER) cc_final: 0.4339 (m-10) REVERT: B 225 MET cc_start: 0.8111 (mtt) cc_final: 0.7807 (mtm) REVERT: B 446 MET cc_start: 0.7800 (tpp) cc_final: 0.7359 (tpp) REVERT: B 450 MET cc_start: 0.8629 (tpp) cc_final: 0.8397 (tpp) REVERT: A 736 GLN cc_start: 0.3673 (OUTLIER) cc_final: 0.3141 (tm-30) REVERT: D 83 TYR cc_start: 0.4890 (OUTLIER) cc_final: 0.4221 (m-10) REVERT: D 225 MET cc_start: 0.8106 (mtt) cc_final: 0.7804 (mtm) REVERT: D 385 MET cc_start: 0.8537 (mmm) cc_final: 0.7118 (mtt) REVERT: D 450 MET cc_start: 0.8582 (tpp) cc_final: 0.8328 (tpp) REVERT: C 256 ILE cc_start: 0.9595 (OUTLIER) cc_final: 0.9377 (mm) outliers start: 82 outliers final: 50 residues processed: 258 average time/residue: 0.3558 time to fit residues: 151.9126 Evaluate side-chains 225 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 171 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 98 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 242 optimal weight: 0.0170 chunk 135 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 25838 Z= 0.311 Angle : 0.613 10.496 35068 Z= 0.297 Chirality : 0.043 0.267 3902 Planarity : 0.004 0.039 4368 Dihedral : 8.763 73.699 4389 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.26 % Favored : 92.67 % Rotamer: Outliers : 3.26 % Allowed : 21.29 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3030 helix: 0.55 (0.13), residues: 1732 sheet: -0.34 (0.61), residues: 68 loop : -2.02 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 509 HIS 0.005 0.001 HIS C 241 PHE 0.030 0.001 PHE D 489 TYR 0.021 0.001 TYR C 183 ARG 0.007 0.000 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 177 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4950 (OUTLIER) cc_final: 0.4268 (m-10) REVERT: B 225 MET cc_start: 0.8159 (mtt) cc_final: 0.7874 (mtm) REVERT: B 446 MET cc_start: 0.7805 (tpp) cc_final: 0.7319 (tpp) REVERT: B 450 MET cc_start: 0.8650 (tpp) cc_final: 0.8396 (tpp) REVERT: A 256 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9336 (mm) REVERT: A 736 GLN cc_start: 0.3750 (OUTLIER) cc_final: 0.3210 (tm-30) REVERT: D 83 TYR cc_start: 0.4945 (OUTLIER) cc_final: 0.4263 (m-10) REVERT: D 225 MET cc_start: 0.8119 (mtt) cc_final: 0.7829 (mtm) REVERT: D 385 MET cc_start: 0.8502 (mmm) cc_final: 0.7104 (mtt) REVERT: D 450 MET cc_start: 0.8530 (tpp) cc_final: 0.8329 (tpp) REVERT: C 256 ILE cc_start: 0.9607 (OUTLIER) cc_final: 0.9364 (mm) REVERT: C 345 HIS cc_start: 0.8114 (t70) cc_final: 0.7886 (t-170) REVERT: C 455 MET cc_start: 0.8629 (tmt) cc_final: 0.8420 (tmt) REVERT: C 736 GLN cc_start: 0.3435 (OUTLIER) cc_final: 0.2786 (tm-30) outliers start: 86 outliers final: 60 residues processed: 249 average time/residue: 0.3269 time to fit residues: 135.9021 Evaluate side-chains 228 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 162 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 TRP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 281 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 165 optimal weight: 0.4980 chunk 245 optimal weight: 3.9990 chunk 163 optimal weight: 20.0000 chunk 291 optimal weight: 0.9990 chunk 182 optimal weight: 0.0470 chunk 177 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25838 Z= 0.190 Angle : 0.579 9.442 35068 Z= 0.279 Chirality : 0.041 0.277 3902 Planarity : 0.003 0.038 4368 Dihedral : 8.494 72.038 4389 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.63 % Favored : 93.30 % Rotamer: Outliers : 3.03 % Allowed : 21.86 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 3030 helix: 0.66 (0.13), residues: 1734 sheet: -0.25 (0.60), residues: 68 loop : -1.95 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 566 HIS 0.004 0.001 HIS C 34 PHE 0.012 0.001 PHE A 315 TYR 0.016 0.001 TYR C 183 ARG 0.005 0.000 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 171 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4931 (OUTLIER) cc_final: 0.4221 (m-10) REVERT: B 225 MET cc_start: 0.8154 (mtt) cc_final: 0.7872 (mtm) REVERT: B 446 MET cc_start: 0.7793 (tpp) cc_final: 0.7303 (tpp) REVERT: B 450 MET cc_start: 0.8716 (tpp) cc_final: 0.8462 (tpp) REVERT: A 256 ILE cc_start: 0.9553 (OUTLIER) cc_final: 0.9316 (mm) REVERT: A 736 GLN cc_start: 0.3729 (OUTLIER) cc_final: 0.3185 (tm-30) REVERT: D 83 TYR cc_start: 0.4975 (OUTLIER) cc_final: 0.4266 (m-10) REVERT: D 100 MET cc_start: 0.8514 (mtt) cc_final: 0.7791 (mpp) REVERT: D 225 MET cc_start: 0.8156 (mtt) cc_final: 0.7876 (mtm) REVERT: D 344 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7411 (p90) REVERT: D 385 MET cc_start: 0.8496 (mmm) cc_final: 0.7572 (mtt) REVERT: D 450 MET cc_start: 0.8674 (tpp) cc_final: 0.8457 (tpp) REVERT: C 256 ILE cc_start: 0.9597 (OUTLIER) cc_final: 0.9377 (mm) REVERT: C 636 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8889 (p0) REVERT: C 736 GLN cc_start: 0.3415 (OUTLIER) cc_final: 0.2761 (tm-30) outliers start: 80 outliers final: 57 residues processed: 240 average time/residue: 0.3292 time to fit residues: 131.9508 Evaluate side-chains 233 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 168 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 6.9990 chunk 116 optimal weight: 0.4980 chunk 173 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25838 Z= 0.138 Angle : 0.559 9.481 35068 Z= 0.268 Chirality : 0.040 0.279 3902 Planarity : 0.003 0.039 4368 Dihedral : 8.081 69.632 4389 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.77 % Favored : 93.17 % Rotamer: Outliers : 2.65 % Allowed : 22.08 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 3030 helix: 0.84 (0.13), residues: 1708 sheet: 0.28 (0.52), residues: 86 loop : -1.84 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 509 HIS 0.003 0.001 HIS C 345 PHE 0.025 0.001 PHE B 489 TYR 0.013 0.001 TYR F 396 ARG 0.006 0.000 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 180 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.4996 (OUTLIER) cc_final: 0.4225 (m-10) REVERT: B 225 MET cc_start: 0.8154 (mtt) cc_final: 0.7871 (mtm) REVERT: B 446 MET cc_start: 0.7736 (tpp) cc_final: 0.7211 (tpp) REVERT: B 508 MET cc_start: 0.8213 (mmm) cc_final: 0.7601 (mmm) REVERT: A 256 ILE cc_start: 0.9547 (OUTLIER) cc_final: 0.9307 (mm) REVERT: A 636 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8876 (p0) REVERT: D 83 TYR cc_start: 0.5086 (OUTLIER) cc_final: 0.4389 (m-10) REVERT: D 96 PHE cc_start: 0.7296 (t80) cc_final: 0.6854 (t80) REVERT: D 100 MET cc_start: 0.8430 (mtt) cc_final: 0.7733 (mpp) REVERT: D 225 MET cc_start: 0.8155 (mtt) cc_final: 0.7874 (mtm) REVERT: D 450 MET cc_start: 0.8773 (tpp) cc_final: 0.8501 (tpp) REVERT: C 256 ILE cc_start: 0.9594 (OUTLIER) cc_final: 0.9340 (mm) REVERT: C 636 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8866 (p0) REVERT: F 398 ASP cc_start: 0.7268 (m-30) cc_final: 0.6663 (t0) outliers start: 70 outliers final: 51 residues processed: 240 average time/residue: 0.3262 time to fit residues: 131.1044 Evaluate side-chains 225 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 168 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 264 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 254 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 270 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25838 Z= 0.177 Angle : 0.568 9.639 35068 Z= 0.272 Chirality : 0.041 0.278 3902 Planarity : 0.003 0.040 4368 Dihedral : 7.878 66.755 4386 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer: Outliers : 2.65 % Allowed : 22.35 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 3030 helix: 0.90 (0.13), residues: 1708 sheet: 0.17 (0.51), residues: 88 loop : -1.83 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 509 HIS 0.004 0.001 HIS A 34 PHE 0.012 0.001 PHE C 315 TYR 0.015 0.001 TYR C 183 ARG 0.006 0.000 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 181 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.5035 (OUTLIER) cc_final: 0.4283 (m-10) REVERT: B 225 MET cc_start: 0.8155 (mtt) cc_final: 0.7874 (mtm) REVERT: B 446 MET cc_start: 0.7745 (tpp) cc_final: 0.7259 (tpp) REVERT: B 450 MET cc_start: 0.8649 (tpp) cc_final: 0.8354 (tpp) REVERT: B 496 MET cc_start: 0.4541 (ptp) cc_final: 0.3963 (ptm) REVERT: B 508 MET cc_start: 0.8214 (mmm) cc_final: 0.7592 (mmm) REVERT: A 256 ILE cc_start: 0.9556 (OUTLIER) cc_final: 0.9313 (mm) REVERT: A 636 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8883 (p0) REVERT: A 736 GLN cc_start: 0.3662 (OUTLIER) cc_final: 0.3142 (tm-30) REVERT: E 409 GLN cc_start: 0.9142 (mt0) cc_final: 0.8910 (mt0) REVERT: D 83 TYR cc_start: 0.5083 (OUTLIER) cc_final: 0.4408 (m-10) REVERT: D 96 PHE cc_start: 0.7271 (t80) cc_final: 0.6833 (t80) REVERT: D 100 MET cc_start: 0.8362 (mtt) cc_final: 0.7697 (mpp) REVERT: D 225 MET cc_start: 0.8161 (mtt) cc_final: 0.7881 (mtm) REVERT: D 450 MET cc_start: 0.8776 (tpp) cc_final: 0.8549 (tpp) REVERT: C 256 ILE cc_start: 0.9575 (OUTLIER) cc_final: 0.9332 (mm) REVERT: C 636 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8888 (p0) REVERT: F 398 ASP cc_start: 0.7272 (m-30) cc_final: 0.6674 (t0) outliers start: 70 outliers final: 55 residues processed: 242 average time/residue: 0.3457 time to fit residues: 140.7853 Evaluate side-chains 239 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 177 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 178 optimal weight: 3.9990 chunk 286 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 136 optimal weight: 0.0570 chunk 199 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 276 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 25838 Z= 0.141 Angle : 0.569 11.912 35068 Z= 0.271 Chirality : 0.040 0.284 3902 Planarity : 0.003 0.040 4368 Dihedral : 7.671 63.124 4386 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 2.50 % Allowed : 22.65 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 3030 helix: 0.95 (0.13), residues: 1706 sheet: 0.05 (0.52), residues: 92 loop : -1.77 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 509 HIS 0.003 0.001 HIS A 34 PHE 0.026 0.001 PHE D 489 TYR 0.013 0.001 TYR C 183 ARG 0.011 0.000 ARG E 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 188 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 TYR cc_start: 0.5012 (OUTLIER) cc_final: 0.4259 (m-10) REVERT: B 225 MET cc_start: 0.8103 (mtt) cc_final: 0.7818 (mtm) REVERT: B 446 MET cc_start: 0.7750 (tpp) cc_final: 0.7233 (tpp) REVERT: B 450 MET cc_start: 0.8645 (tpp) cc_final: 0.8340 (tpp) REVERT: B 496 MET cc_start: 0.4540 (ptp) cc_final: 0.3990 (ptm) REVERT: B 508 MET cc_start: 0.8210 (mmm) cc_final: 0.7600 (mmm) REVERT: A 256 ILE cc_start: 0.9547 (OUTLIER) cc_final: 0.9308 (mm) REVERT: A 636 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8859 (p0) REVERT: A 736 GLN cc_start: 0.3633 (OUTLIER) cc_final: 0.3127 (tm-30) REVERT: E 406 GLU cc_start: 0.8901 (pm20) cc_final: 0.8676 (pm20) REVERT: E 409 GLN cc_start: 0.9178 (mt0) cc_final: 0.8960 (mt0) REVERT: D 83 TYR cc_start: 0.5098 (OUTLIER) cc_final: 0.4414 (m-10) REVERT: D 96 PHE cc_start: 0.7259 (t80) cc_final: 0.6774 (t80) REVERT: D 100 MET cc_start: 0.8360 (mtt) cc_final: 0.7692 (mpp) REVERT: D 225 MET cc_start: 0.8113 (mtt) cc_final: 0.7830 (mtm) REVERT: D 450 MET cc_start: 0.8769 (tpp) cc_final: 0.8505 (tpp) REVERT: D 508 MET cc_start: 0.8259 (mmm) cc_final: 0.7649 (mmm) REVERT: C 256 ILE cc_start: 0.9567 (OUTLIER) cc_final: 0.9316 (mm) REVERT: C 636 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8864 (p0) REVERT: F 398 ASP cc_start: 0.7271 (m-30) cc_final: 0.6629 (t0) outliers start: 66 outliers final: 48 residues processed: 245 average time/residue: 0.3409 time to fit residues: 136.1313 Evaluate side-chains 231 residues out of total 2640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 176 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain E residue 371 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain F residue 357 ARG Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 190 optimal weight: 10.0000 chunk 255 optimal weight: 0.0070 chunk 73 optimal weight: 0.9980 chunk 220 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 239 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS ** D 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.126320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.075997 restraints weight = 59074.097| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.97 r_work: 0.2912 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 25838 Z= 0.132 Angle : 0.563 11.525 35068 Z= 0.267 Chirality : 0.040 0.278 3902 Planarity : 0.003 0.040 4368 Dihedral : 7.410 59.716 4386 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 1.97 % Allowed : 23.14 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 3030 helix: 1.04 (0.13), residues: 1704 sheet: 0.01 (0.53), residues: 94 loop : -1.68 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 168 HIS 0.004 0.001 HIS C 345 PHE 0.011 0.001 PHE C 315 TYR 0.023 0.001 TYR E 396 ARG 0.009 0.000 ARG F 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5841.79 seconds wall clock time: 106 minutes 48.00 seconds (6408.00 seconds total)