Starting phenix.real_space_refine on Wed Feb 21 18:23:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/02_2024/7yr2_34043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/02_2024/7yr2_34043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/02_2024/7yr2_34043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/02_2024/7yr2_34043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/02_2024/7yr2_34043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/02_2024/7yr2_34043.pdb" } resolution = 3.3 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= 0.033 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 1 6.06 5 S 140 5.16 5 Cl 1 4.86 5 C 20008 2.51 5 N 5142 2.21 5 O 6200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 145": "OE1" <-> "OE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 661": "OE1" <-> "OE2" Residue "D PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 988": "OE1" <-> "OE2" Residue "D GLU 990": "OE1" <-> "OE2" Residue "D GLU 1111": "OE1" <-> "OE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E ASP 398": "OD1" <-> "OD2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 578": "OD1" <-> "OD2" Residue "E ASP 745": "OD1" <-> "OD2" Residue "E GLU 773": "OE1" <-> "OE2" Residue "E ASP 979": "OD1" <-> "OD2" Residue "E GLU 988": "OE1" <-> "OE2" Residue "E GLU 990": "OE1" <-> "OE2" Residue "E GLU 1092": "OE1" <-> "OE2" Residue "E ASP 1118": "OD1" <-> "OD2" Residue "E TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "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: 31492 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "D" Number of atoms: 8535 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1097, 8530 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 42 Conformer: "B" Number of residues, atoms: 1097, 8530 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 8729 Chain: "E" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8540 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 8536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8536 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: "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: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG D 78 " occ=0.51 ... (8 atoms not shown) pdb=" CB BARG D 78 " occ=0.49 Time building chain proxies: 19.65, per 1000 atoms: 0.62 Number of scatterers: 31492 At special positions: 0 Unit cell: (156, 173.68, 237.12, 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 1 29.99 Cl 1 17.00 S 140 16.00 O 6200 8.00 N 5142 7.00 C 20008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.02 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " 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-ASN " NAG A 903 " - " ASN A 546 " " NAG A 904 " - " ASN A 90 " " NAG A 905 " - " ASN A 322 " " NAG A 906 " - " ASN A 53 " " NAG B 1 " - " ASN D 717 " " NAG C1301 " - " ASN C 61 " " NAG C1311 " - " ASN C 616 " " NAG C1313 " - " ASN C 709 " " NAG C1315 " - " ASN C1134 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 74 " " NAG D1303 " - " ASN D 122 " " NAG D1304 " - " ASN D 149 " " NAG D1305 " - " ASN D 165 " " NAG D1306 " - " ASN D 234 " " NAG D1307 " - " ASN D 282 " " NAG D1308 " - " ASN D 331 " " NAG D1310 " - " ASN D 603 " " NAG D1311 " - " ASN D 616 " " NAG D1312 " - " ASN D 657 " " NAG D1313 " - " ASN D 709 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 74 " " NAG E1303 " - " ASN E 122 " " NAG E1304 " - " ASN E 149 " " NAG E1305 " - " ASN E 165 " " NAG E1306 " - " ASN E 234 " " NAG E1307 " - " ASN E 282 " " NAG E1308 " - " ASN E 331 " " NAG E1309 " - " ASN E 343 " " NAG E1310 " - " ASN E 603 " " NAG E1311 " - " ASN E 616 " " NAG E1312 " - " ASN E 657 " " NAG E1313 " - " ASN E 709 " " NAG E1314 " - " ASN E1098 " " NAG E1315 " - " ASN E1134 " " NAG F 1 " - " ASN D 801 " " NAG G 1 " - " ASN D1074 " " NAG H 1 " - " ASN E 717 " " NAG I 1 " - " ASN E 801 " " NAG J 1 " - " ASN E1074 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 801 " " NAG M 1 " - " ASN C1074 " Time building additional restraints: 12.16 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7294 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 53 sheets defined 27.6% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.270A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.799A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.841A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.576A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.692A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.701A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.744A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 384 Processing helix chain 'A' and resid 399 through 413 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.391A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.119A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.542A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.487A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.052A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.808A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 760 through 783 removed outlier: 3.513A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 869 through 884 removed outlier: 3.624A pdb=" N THR D 883 " --> pdb=" O ALA D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 918 Processing helix chain 'D' and resid 919 through 941 removed outlier: 4.555A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.610A pdb=" N GLN D 965 " --> pdb=" O THR D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 983 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.336A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D1002 " --> pdb=" O THR D 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 removed outlier: 3.533A pdb=" N LEU E 303 " --> pdb=" O THR E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.499A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.558A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 746 through 755 Processing helix chain 'E' and resid 759 through 783 removed outlier: 3.668A pdb=" N LEU E 763 " --> pdb=" O PHE E 759 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 851 through 855 removed outlier: 3.569A pdb=" N PHE E 855 " --> pdb=" O ALA E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 869 through 884 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 941 removed outlier: 4.401A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.552A pdb=" N ASN E 955 " --> pdb=" O VAL E 951 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1032 removed outlier: 4.541A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.668A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.718A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.765A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.604A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 869 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.512A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.637A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 6.998A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.526A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.775A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.096A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.945A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'D' and resid 26 through 30 removed outlier: 4.346A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.848A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.747A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'D' and resid 311 through 318 removed outlier: 7.565A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 325 through 326 removed outlier: 3.620A pdb=" N ASN D 542 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 539 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.632A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 452 through 454 removed outlier: 4.042A pdb=" N TYR D 453 " --> pdb=" O GLN D 493 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 575 through 577 Processing sheet with id=AB4, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.642A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER D 691 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.550A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 718 through 728 removed outlier: 7.324A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 733 through 735 removed outlier: 4.395A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'D' and resid 1088 through 1090 Processing sheet with id=AC2, first strand: chain 'E' and resid 28 through 30 removed outlier: 3.528A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR E 91 " --> pdb=" O GLY E 268 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 208 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 50 through 55 removed outlier: 4.240A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 168 through 169 removed outlier: 3.821A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 311 through 319 removed outlier: 7.093A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AC7, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.167A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.352A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'E' and resid 565 through 566 removed outlier: 7.099A pdb=" N PHE E 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.732A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 702 through 704 removed outlier: 3.736A pdb=" N LYS C 790 " --> pdb=" O ASN E 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'E' and resid 718 through 727 removed outlier: 7.073A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 733 through 735 removed outlier: 4.377A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 1081 through 1082 Processing sheet with id=AD8, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.509A pdb=" N SER C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.806A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.943A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 201 through 202 removed outlier: 3.781A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.323A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.692A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.043A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.366A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.763A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 659 through 660 removed outlier: 4.489A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 674 through 675 Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.012A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 1073 hydrogen bonds defined for protein. 2991 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: 11.62 Time building geometry restraints manager: 12.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.08: 1 1.08 - 1.27: 5101 1.27 - 1.46: 12806 1.46 - 1.65: 14076 1.65 - 1.85: 189 Bond restraints: 32173 Sorted by residual: bond pdb=" CG PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 1.503 0.890 0.613 3.40e-02 8.65e+02 3.25e+02 bond pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 1.473 1.606 -0.133 1.40e-02 5.10e+03 9.02e+01 bond pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 1.492 1.846 -0.354 5.00e-02 4.00e+02 5.00e+01 bond pdb=" N PRO A 321 " pdb=" CA PRO A 321 " ideal model delta sigma weight residual 1.466 1.404 0.063 1.17e-02 7.31e+03 2.86e+01 bond pdb=" C1 NAG E1303 " pdb=" O5 NAG E1303 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 32168 not shown) Histogram of bond angle deviations from ideal: 78.91 - 89.99: 2 89.99 - 101.08: 42 101.08 - 112.16: 16730 112.16 - 123.25: 25578 123.25 - 134.33: 1453 Bond angle restraints: 43805 Sorted by residual: angle pdb=" N PRO A 321 " pdb=" CD PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 103.20 78.91 24.29 1.50e+00 4.44e-01 2.62e+02 angle pdb=" CA PRO A 321 " pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 112.00 94.34 17.66 1.40e+00 5.10e-01 1.59e+02 angle pdb=" N ASN D 331 " pdb=" CA ASN D 331 " pdb=" C ASN D 331 " ideal model delta sigma weight residual 111.71 97.76 13.95 1.15e+00 7.56e-01 1.47e+02 angle pdb=" CA PRO A 321 " pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 104.50 84.26 20.24 1.90e+00 2.77e-01 1.14e+02 angle pdb=" N PRO D 330 " pdb=" CA PRO D 330 " pdb=" C PRO D 330 " ideal model delta sigma weight residual 112.47 125.47 -13.00 2.06e+00 2.36e-01 3.98e+01 ... (remaining 43800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 18852 24.93 - 49.85: 957 49.85 - 74.78: 154 74.78 - 99.71: 33 99.71 - 124.63: 4 Dihedral angle restraints: 20000 sinusoidal: 8651 harmonic: 11349 Sorted by residual: dihedral pdb=" CB CYS D 738 " pdb=" SG CYS D 738 " pdb=" SG CYS D 760 " pdb=" CB CYS D 760 " ideal model delta sinusoidal sigma weight residual 93.00 -178.79 -88.21 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS E 662 " pdb=" SG CYS E 662 " pdb=" SG CYS E 671 " pdb=" CB CYS E 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.86 -83.14 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 21.16 71.84 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 19997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4699 0.090 - 0.181: 363 0.181 - 0.271: 8 0.271 - 0.362: 4 0.362 - 0.452: 5 Chirality restraints: 5079 Sorted by residual: chirality pdb=" C1 NAG D1301 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG D1301 " pdb=" O5 NAG D1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN E 801 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN D 801 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 5076 not shown) Planarity restraints: 5639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " -0.112 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO A 321 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 328 " 0.025 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C ARG D 328 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG D 328 " 0.033 2.00e-02 2.50e+03 pdb=" N PHE D 329 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 122 " 0.006 2.00e-02 2.50e+03 3.23e-02 1.30e+01 pdb=" CG ASN D 122 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN D 122 " 0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN D 122 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG D1303 " 0.030 2.00e-02 2.50e+03 ... (remaining 5636 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 580 2.66 - 3.22: 29861 3.22 - 3.78: 47600 3.78 - 4.34: 64075 4.34 - 4.90: 105860 Nonbonded interactions: 247976 Sorted by model distance: nonbonded pdb=" OD2 ASP D 737 " pdb=" ND2 ASN C 317 " model vdw 2.101 2.520 nonbonded pdb=" O THR D 393 " pdb=" OG1 THR D 523 " model vdw 2.153 2.440 nonbonded pdb=" OD1 ASN C 122 " pdb=" N ALA C 123 " model vdw 2.156 2.520 nonbonded pdb=" OG SER D 116 " pdb=" O CYS D 131 " model vdw 2.161 2.440 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.168 2.230 ... (remaining 247971 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 'B' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 25 through 77 or resid 79 through 189 or (resid 190 and (n \ ame N or name CA or name C or name O or name CB )) or resid 191 through 194 or ( \ resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ through 327 or (resid 328 through 329 and (name N or name CA or name C or name O \ or name CB )) or resid 330 through 1144 or resid 1301 through 1315)) selection = (chain 'D' and (resid 25 through 77 or resid 79 through 95 or (resid 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 189 or (res \ id 190 and (name N or name CA or name C or name O or name CB )) or resid 191 thr \ ough 346 or (resid 347 through 348 and (name N or name CA or name C or name O or \ name CB )) or resid 349 through 1144 or resid 1301 through 1315)) selection = (chain 'E' and (resid 25 through 77 or resid 79 through 95 or (resid 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 194 or (res \ id 195 and (name N or name CA or name C or name O or name CB )) or resid 196 thr \ ough 327 or (resid 328 through 329 and (name N or name CA or name C or name O or \ name CB )) or resid 330 through 346 or (resid 347 through 348 and (name N or na \ me CA or name C or name O or name CB )) or resid 349 through 1144 or resid 1301 \ through 1315)) } 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=0.49 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 9.000 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 88.310 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.280 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.005 0.613 32173 Z= 0.381 Angle : 0.687 24.290 43805 Z= 0.369 Chirality : 0.048 0.452 5079 Planarity : 0.005 0.152 5595 Dihedral : 14.563 124.632 12589 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.03 % Favored : 92.79 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.35 (0.13), residues: 3871 helix: 0.83 (0.17), residues: 1008 sheet: -0.60 (0.20), residues: 592 loop : -1.87 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 271 HIS 0.008 0.001 HIS A 374 PHE 0.019 0.001 PHE C 490 TYR 0.032 0.001 TYR C 495 ARG 0.005 0.000 ARG D1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 321 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4352 (ppp) cc_final: 0.2022 (ttt) REVERT: A 249 MET cc_start: 0.1329 (tmm) cc_final: 0.0828 (tmm) REVERT: A 360 MET cc_start: -0.1243 (tpt) cc_final: -0.2029 (ptt) REVERT: A 480 MET cc_start: 0.0779 (mtt) cc_final: 0.0453 (mtt) REVERT: D 578 ASP cc_start: 0.5818 (t0) cc_final: 0.5538 (t0) REVERT: D 950 ASP cc_start: 0.7306 (m-30) cc_final: 0.6965 (m-30) REVERT: E 389 ASP cc_start: 0.7465 (p0) cc_final: 0.7254 (p0) REVERT: E 867 ASP cc_start: 0.7597 (m-30) cc_final: 0.7130 (m-30) REVERT: C 574 ASP cc_start: 0.8257 (t70) cc_final: 0.7493 (t0) REVERT: C 950 ASP cc_start: 0.7682 (m-30) cc_final: 0.7398 (m-30) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.3667 time to fit residues: 201.4939 Evaluate side-chains 224 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 325 optimal weight: 4.9990 chunk 292 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 197 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 chunk 302 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 225 optimal weight: 0.9990 chunk 350 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 154 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN E 450 ASN ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN C 394 ASN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32173 Z= 0.226 Angle : 0.594 11.431 43805 Z= 0.301 Chirality : 0.045 0.251 5079 Planarity : 0.004 0.059 5595 Dihedral : 8.369 113.993 5580 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.60 % Favored : 92.35 % Rotamer: Outliers : 1.24 % Allowed : 6.22 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.18 (0.13), residues: 3871 helix: 1.04 (0.17), residues: 998 sheet: -0.67 (0.20), residues: 588 loop : -1.74 (0.13), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 271 HIS 0.008 0.001 HIS A 374 PHE 0.029 0.001 PHE D 541 TYR 0.025 0.001 TYR C 495 ARG 0.004 0.000 ARG D1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 260 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4298 (ppp) cc_final: 0.2044 (ttt) REVERT: A 249 MET cc_start: 0.1427 (tmm) cc_final: 0.0891 (tmm) REVERT: A 323 MET cc_start: 0.0698 (mmm) cc_final: 0.0383 (mtm) REVERT: A 360 MET cc_start: -0.1329 (tpt) cc_final: -0.2266 (ptt) REVERT: A 480 MET cc_start: 0.0763 (mtt) cc_final: 0.0529 (mtt) REVERT: D 578 ASP cc_start: 0.5739 (t0) cc_final: 0.5432 (t0) REVERT: D 902 MET cc_start: 0.8494 (tpp) cc_final: 0.8212 (mmt) REVERT: E 389 ASP cc_start: 0.7493 (p0) cc_final: 0.7241 (p0) REVERT: E 723 THR cc_start: 0.8820 (t) cc_final: 0.8574 (p) REVERT: C 26 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7277 (tm-30) REVERT: C 574 ASP cc_start: 0.8250 (t70) cc_final: 0.7457 (t0) REVERT: C 950 ASP cc_start: 0.7691 (m-30) cc_final: 0.7452 (m-30) REVERT: C 1071 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8732 (pm20) outliers start: 42 outliers final: 28 residues processed: 289 average time/residue: 0.3848 time to fit residues: 189.9491 Evaluate side-chains 259 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 230 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1100 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 194 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 291 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 351 optimal weight: 3.9990 chunk 379 optimal weight: 0.9990 chunk 312 optimal weight: 3.9990 chunk 348 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 281 optimal weight: 0.3980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN D 580 GLN D 607 GLN E 493 GLN ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32173 Z= 0.195 Angle : 0.563 9.539 43805 Z= 0.284 Chirality : 0.044 0.247 5079 Planarity : 0.004 0.058 5595 Dihedral : 7.493 110.094 5580 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 1.45 % Allowed : 8.65 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -1.11 (0.13), residues: 3871 helix: 1.13 (0.17), residues: 1011 sheet: -0.65 (0.20), residues: 581 loop : -1.71 (0.13), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 271 HIS 0.008 0.001 HIS A 374 PHE 0.017 0.001 PHE D 541 TYR 0.022 0.001 TYR C 265 ARG 0.003 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 254 time to evaluate : 3.621 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.2264 (mt0) cc_final: 0.1578 (pp30) REVERT: A 82 MET cc_start: 0.4404 (ppp) cc_final: 0.2161 (ttt) REVERT: A 249 MET cc_start: 0.1400 (tmm) cc_final: 0.0885 (tmm) REVERT: A 310 GLU cc_start: 0.1139 (OUTLIER) cc_final: 0.0250 (tm-30) REVERT: A 360 MET cc_start: -0.1556 (tpt) cc_final: -0.2364 (ptt) REVERT: A 480 MET cc_start: 0.0749 (mtt) cc_final: 0.0505 (mtt) REVERT: D 542 ASN cc_start: 0.7205 (t0) cc_final: 0.6513 (t0) REVERT: D 902 MET cc_start: 0.8470 (tpp) cc_final: 0.8143 (mmt) REVERT: E 389 ASP cc_start: 0.7502 (p0) cc_final: 0.7228 (p0) REVERT: E 723 THR cc_start: 0.8802 (t) cc_final: 0.8541 (p) REVERT: E 739 THR cc_start: 0.8604 (m) cc_final: 0.8345 (p) REVERT: C 26 GLN cc_start: 0.7645 (tm-30) cc_final: 0.7292 (tm-30) REVERT: C 456 PHE cc_start: 0.8175 (m-10) cc_final: 0.7942 (m-80) REVERT: C 950 ASP cc_start: 0.7725 (m-30) cc_final: 0.7474 (m-30) outliers start: 49 outliers final: 30 residues processed: 288 average time/residue: 0.3943 time to fit residues: 193.7147 Evaluate side-chains 265 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 346 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 167 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 352 optimal weight: 0.8980 chunk 373 optimal weight: 0.7980 chunk 184 optimal weight: 10.0000 chunk 334 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN ** D 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN ** E 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN C 183 GLN C 370 ASN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32173 Z= 0.237 Angle : 0.574 9.699 43805 Z= 0.289 Chirality : 0.044 0.258 5079 Planarity : 0.004 0.059 5595 Dihedral : 6.920 103.256 5580 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.07 % Favored : 91.91 % Rotamer: Outliers : 1.87 % Allowed : 10.64 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -1.15 (0.13), residues: 3871 helix: 1.16 (0.17), residues: 1004 sheet: -0.79 (0.20), residues: 576 loop : -1.73 (0.13), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 271 HIS 0.008 0.001 HIS A 374 PHE 0.016 0.001 PHE D 855 TYR 0.023 0.001 TYR C 265 ARG 0.012 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 253 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4309 (ppp) cc_final: 0.2140 (ttt) REVERT: A 249 MET cc_start: 0.1588 (tmm) cc_final: 0.1005 (tmm) REVERT: A 360 MET cc_start: -0.1812 (tpt) cc_final: -0.2637 (ptp) REVERT: A 480 MET cc_start: 0.0729 (mtt) cc_final: 0.0500 (mtt) REVERT: D 158 ARG cc_start: 0.8233 (ttm170) cc_final: 0.7450 (mmt90) REVERT: D 542 ASN cc_start: 0.7278 (t0) cc_final: 0.6550 (t0) REVERT: E 389 ASP cc_start: 0.7611 (p0) cc_final: 0.7298 (p0) REVERT: E 451 TYR cc_start: 0.5279 (m-10) cc_final: 0.4664 (m-10) REVERT: E 697 MET cc_start: 0.8235 (ptm) cc_final: 0.7962 (ptp) REVERT: C 26 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7309 (tm-30) REVERT: C 950 ASP cc_start: 0.7730 (m-30) cc_final: 0.7453 (m-30) outliers start: 63 outliers final: 46 residues processed: 299 average time/residue: 0.3915 time to fit residues: 197.9455 Evaluate side-chains 279 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 233 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain E residue 826 VAL Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1100 THR Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 310 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 318 optimal weight: 1.9990 chunk 257 optimal weight: 0.0000 chunk 0 optimal weight: 30.0000 chunk 190 optimal weight: 0.7980 chunk 334 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 98 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 552 GLN D 607 GLN E 52 GLN E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN E 658 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32173 Z= 0.175 Angle : 0.548 9.653 43805 Z= 0.276 Chirality : 0.043 0.248 5079 Planarity : 0.004 0.059 5595 Dihedral : 6.542 99.803 5580 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.76 % Favored : 92.19 % Rotamer: Outliers : 1.60 % Allowed : 12.15 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -1.05 (0.13), residues: 3871 helix: 1.27 (0.17), residues: 1011 sheet: -0.68 (0.20), residues: 584 loop : -1.70 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 271 HIS 0.007 0.001 HIS A 374 PHE 0.024 0.001 PHE A 72 TYR 0.021 0.001 TYR C 265 ARG 0.004 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 249 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4311 (ppp) cc_final: 0.2135 (mtt) REVERT: A 249 MET cc_start: 0.1546 (tmm) cc_final: 0.0978 (tmm) REVERT: A 360 MET cc_start: -0.1773 (tpt) cc_final: -0.2736 (ptp) REVERT: A 480 MET cc_start: 0.0755 (mtt) cc_final: 0.0526 (mtt) REVERT: D 158 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7427 (mmt90) REVERT: D 542 ASN cc_start: 0.7188 (t0) cc_final: 0.6526 (t0) REVERT: E 41 LYS cc_start: 0.7786 (tptm) cc_final: 0.7207 (tptm) REVERT: E 314 GLN cc_start: 0.8180 (tt0) cc_final: 0.7905 (tt0) REVERT: E 389 ASP cc_start: 0.7600 (p0) cc_final: 0.7294 (p0) REVERT: E 697 MET cc_start: 0.8194 (ptm) cc_final: 0.7955 (ptp) REVERT: C 26 GLN cc_start: 0.7573 (tm-30) cc_final: 0.6866 (tm-30) REVERT: C 233 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6720 (mp) REVERT: C 950 ASP cc_start: 0.7728 (m-30) cc_final: 0.7451 (m-30) REVERT: C 1050 MET cc_start: 0.8499 (ptm) cc_final: 0.8274 (ptp) outliers start: 54 outliers final: 46 residues processed: 286 average time/residue: 0.3732 time to fit residues: 182.7287 Evaluate side-chains 282 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 235 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 125 optimal weight: 4.9990 chunk 336 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 373 optimal weight: 0.6980 chunk 310 optimal weight: 0.0980 chunk 172 optimal weight: 0.7980 chunk 31 optimal weight: 0.0570 chunk 123 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32173 Z= 0.146 Angle : 0.532 9.792 43805 Z= 0.267 Chirality : 0.043 0.252 5079 Planarity : 0.004 0.060 5595 Dihedral : 6.060 93.682 5580 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.42 % Favored : 92.53 % Rotamer: Outliers : 1.90 % Allowed : 12.51 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.96 (0.13), residues: 3871 helix: 1.43 (0.17), residues: 1006 sheet: -0.59 (0.20), residues: 611 loop : -1.71 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 271 HIS 0.007 0.001 HIS A 374 PHE 0.019 0.001 PHE A 72 TYR 0.019 0.001 TYR A 255 ARG 0.003 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 253 time to evaluate : 3.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4380 (ppp) cc_final: 0.2048 (mtt) REVERT: A 249 MET cc_start: 0.1547 (tmm) cc_final: 0.1006 (tmm) REVERT: A 360 MET cc_start: -0.1777 (tpt) cc_final: -0.2794 (ptt) REVERT: A 366 MET cc_start: -0.0236 (mtp) cc_final: -0.0538 (tpp) REVERT: A 480 MET cc_start: 0.0824 (mtt) cc_final: 0.0565 (mtt) REVERT: D 158 ARG cc_start: 0.8109 (ttm170) cc_final: 0.7427 (mmt90) REVERT: D 542 ASN cc_start: 0.7165 (t0) cc_final: 0.6458 (t0) REVERT: D 902 MET cc_start: 0.8522 (tpp) cc_final: 0.8292 (mmt) REVERT: D 950 ASP cc_start: 0.7240 (m-30) cc_final: 0.6680 (m-30) REVERT: E 314 GLN cc_start: 0.8110 (tt0) cc_final: 0.7834 (tt0) REVERT: E 389 ASP cc_start: 0.7518 (p0) cc_final: 0.7238 (p0) REVERT: E 395 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8226 (t) REVERT: C 26 GLN cc_start: 0.7403 (tm-30) cc_final: 0.7094 (tt0) REVERT: C 878 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7767 (mp) REVERT: C 950 ASP cc_start: 0.7703 (m-30) cc_final: 0.7426 (m-30) REVERT: C 1050 MET cc_start: 0.8514 (ptm) cc_final: 0.8292 (ptp) outliers start: 64 outliers final: 43 residues processed: 302 average time/residue: 0.3754 time to fit residues: 194.5163 Evaluate side-chains 281 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 236 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 1100 THR Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 360 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 212 optimal weight: 0.7980 chunk 272 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 372 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 226 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 926 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32173 Z= 0.191 Angle : 0.545 10.412 43805 Z= 0.274 Chirality : 0.044 0.254 5079 Planarity : 0.004 0.061 5595 Dihedral : 5.900 87.467 5580 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.65 % Favored : 92.30 % Rotamer: Outliers : 2.02 % Allowed : 12.80 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.95 (0.13), residues: 3871 helix: 1.48 (0.17), residues: 992 sheet: -0.60 (0.20), residues: 613 loop : -1.70 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 271 HIS 0.006 0.001 HIS A 374 PHE 0.030 0.001 PHE C 855 TYR 0.020 0.001 TYR C 265 ARG 0.003 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 246 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4325 (ppp) cc_final: 0.1935 (mtt) REVERT: A 249 MET cc_start: 0.1419 (tmm) cc_final: 0.0858 (tmm) REVERT: A 360 MET cc_start: -0.2063 (tpt) cc_final: -0.3025 (ptp) REVERT: A 480 MET cc_start: 0.0838 (mtt) cc_final: 0.0549 (mtt) REVERT: D 238 PHE cc_start: 0.4420 (t80) cc_final: 0.4175 (t80) REVERT: D 542 ASN cc_start: 0.7207 (t0) cc_final: 0.6488 (t0) REVERT: D 578 ASP cc_start: 0.5736 (t0) cc_final: 0.5304 (t0) REVERT: E 41 LYS cc_start: 0.7811 (tptm) cc_final: 0.7228 (tptm) REVERT: E 314 GLN cc_start: 0.8168 (tt0) cc_final: 0.7885 (tt0) REVERT: E 389 ASP cc_start: 0.7566 (p0) cc_final: 0.7256 (p0) REVERT: E 409 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: E 455 LEU cc_start: 0.8118 (mt) cc_final: 0.7755 (mp) REVERT: C 26 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7108 (tt0) REVERT: C 462 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8227 (mttp) REVERT: C 950 ASP cc_start: 0.7717 (m-30) cc_final: 0.7434 (m-30) REVERT: C 1050 MET cc_start: 0.8557 (ptm) cc_final: 0.8338 (ptp) outliers start: 68 outliers final: 55 residues processed: 299 average time/residue: 0.3772 time to fit residues: 194.0648 Evaluate side-chains 290 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 234 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 826 VAL Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1100 THR Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 230 optimal weight: 0.0970 chunk 148 optimal weight: 0.9980 chunk 222 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 292 optimal weight: 0.8980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 32173 Z= 0.164 Angle : 0.542 10.773 43805 Z= 0.271 Chirality : 0.043 0.250 5079 Planarity : 0.004 0.062 5595 Dihedral : 5.702 78.229 5580 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.42 % Favored : 92.53 % Rotamer: Outliers : 1.99 % Allowed : 13.01 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.90 (0.13), residues: 3871 helix: 1.47 (0.17), residues: 1002 sheet: -0.53 (0.20), residues: 600 loop : -1.67 (0.13), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 271 HIS 0.005 0.001 HIS A 374 PHE 0.027 0.001 PHE C 855 TYR 0.020 0.001 TYR C 265 ARG 0.008 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 248 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4285 (ppp) cc_final: 0.1935 (mtt) REVERT: A 249 MET cc_start: 0.1273 (tmm) cc_final: 0.0783 (tmm) REVERT: A 358 ILE cc_start: -0.0446 (mm) cc_final: -0.1016 (tt) REVERT: A 360 MET cc_start: -0.2270 (tpt) cc_final: -0.3281 (ptp) REVERT: A 480 MET cc_start: 0.0802 (mtt) cc_final: 0.0514 (mtt) REVERT: D 158 ARG cc_start: 0.8280 (ttm170) cc_final: 0.7397 (mmt90) REVERT: D 542 ASN cc_start: 0.7234 (t0) cc_final: 0.6479 (t0) REVERT: D 578 ASP cc_start: 0.5823 (t0) cc_final: 0.5330 (t0) REVERT: D 902 MET cc_start: 0.8522 (tpp) cc_final: 0.8294 (mmt) REVERT: D 950 ASP cc_start: 0.7242 (m-30) cc_final: 0.6688 (m-30) REVERT: E 314 GLN cc_start: 0.8166 (tt0) cc_final: 0.7857 (tt0) REVERT: E 389 ASP cc_start: 0.7594 (p0) cc_final: 0.7289 (p0) REVERT: E 395 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8228 (t) REVERT: E 409 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: E 468 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8332 (tt) REVERT: C 26 GLN cc_start: 0.7386 (tm-30) cc_final: 0.6991 (tm-30) REVERT: C 462 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8221 (mttp) REVERT: C 878 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7800 (mp) REVERT: C 950 ASP cc_start: 0.7709 (m-30) cc_final: 0.7426 (m-30) REVERT: C 1050 MET cc_start: 0.8561 (ptm) cc_final: 0.8361 (ptp) outliers start: 67 outliers final: 55 residues processed: 302 average time/residue: 0.3803 time to fit residues: 197.1327 Evaluate side-chains 289 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 230 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 826 VAL Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1100 THR Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 338 optimal weight: 4.9990 chunk 356 optimal weight: 3.9990 chunk 325 optimal weight: 0.0670 chunk 346 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 313 optimal weight: 0.7980 chunk 327 optimal weight: 2.9990 chunk 345 optimal weight: 0.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN E1005 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32173 Z= 0.196 Angle : 0.552 10.759 43805 Z= 0.276 Chirality : 0.044 0.254 5079 Planarity : 0.004 0.062 5595 Dihedral : 5.634 64.731 5580 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.99 % Favored : 91.96 % Rotamer: Outliers : 2.02 % Allowed : 13.37 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.92 (0.13), residues: 3871 helix: 1.46 (0.17), residues: 999 sheet: -0.55 (0.20), residues: 628 loop : -1.68 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 271 HIS 0.005 0.001 HIS A 374 PHE 0.025 0.001 PHE C 855 TYR 0.022 0.001 TYR E 451 ARG 0.003 0.000 ARG E1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 230 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4175 (ppp) cc_final: 0.1861 (mtt) REVERT: A 249 MET cc_start: 0.1482 (tmm) cc_final: 0.0952 (tmm) REVERT: A 358 ILE cc_start: -0.0323 (mm) cc_final: -0.0926 (tt) REVERT: A 360 MET cc_start: -0.2502 (tpt) cc_final: -0.3434 (ptp) REVERT: D 542 ASN cc_start: 0.7277 (t0) cc_final: 0.6858 (t0) REVERT: D 578 ASP cc_start: 0.5823 (t0) cc_final: 0.5350 (t0) REVERT: D 950 ASP cc_start: 0.7267 (m-30) cc_final: 0.6992 (m-30) REVERT: E 314 GLN cc_start: 0.8174 (tt0) cc_final: 0.7878 (tt0) REVERT: E 389 ASP cc_start: 0.7650 (p0) cc_final: 0.7308 (p0) REVERT: E 409 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: E 737 ASP cc_start: 0.7472 (t0) cc_final: 0.7021 (t0) REVERT: E 739 THR cc_start: 0.8503 (m) cc_final: 0.8239 (p) REVERT: C 26 GLN cc_start: 0.7447 (tm-30) cc_final: 0.7153 (tm-30) REVERT: C 950 ASP cc_start: 0.7731 (m-30) cc_final: 0.7439 (m-30) outliers start: 68 outliers final: 62 residues processed: 284 average time/residue: 0.3721 time to fit residues: 182.4777 Evaluate side-chains 289 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 226 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 826 VAL Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain E residue 1041 ASP Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1100 THR Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 227 optimal weight: 0.0270 chunk 366 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 254 optimal weight: 0.7980 chunk 384 optimal weight: 0.8980 chunk 353 optimal weight: 0.2980 chunk 306 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 236 optimal weight: 0.6980 chunk 187 optimal weight: 10.0000 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32173 Z= 0.153 Angle : 0.542 11.018 43805 Z= 0.272 Chirality : 0.043 0.251 5079 Planarity : 0.004 0.062 5595 Dihedral : 5.503 59.046 5580 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.42 % Favored : 92.53 % Rotamer: Outliers : 1.84 % Allowed : 13.75 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.89 (0.14), residues: 3871 helix: 1.47 (0.17), residues: 1007 sheet: -0.49 (0.20), residues: 634 loop : -1.69 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 271 HIS 0.006 0.001 HIS A 374 PHE 0.030 0.001 PHE D 543 TYR 0.020 0.001 TYR C 265 ARG 0.004 0.000 ARG E1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7742 Ramachandran restraints generated. 3871 Oldfield, 0 Emsley, 3871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 233 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.4112 (ppp) cc_final: 0.1810 (mtt) REVERT: A 249 MET cc_start: 0.1423 (tmm) cc_final: 0.0962 (tmm) REVERT: A 310 GLU cc_start: 0.0891 (OUTLIER) cc_final: 0.0179 (tm-30) REVERT: A 360 MET cc_start: -0.2606 (tpt) cc_final: -0.3468 (ptp) REVERT: D 542 ASN cc_start: 0.7375 (t0) cc_final: 0.6670 (t0) REVERT: D 578 ASP cc_start: 0.5863 (t0) cc_final: 0.5430 (t70) REVERT: D 902 MET cc_start: 0.8544 (tpp) cc_final: 0.8329 (mmt) REVERT: D 950 ASP cc_start: 0.7220 (m-30) cc_final: 0.6947 (m-30) REVERT: E 314 GLN cc_start: 0.8200 (tt0) cc_final: 0.7938 (tt0) REVERT: E 389 ASP cc_start: 0.7692 (p0) cc_final: 0.7364 (p0) REVERT: E 395 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8179 (t) REVERT: E 409 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: E 737 ASP cc_start: 0.7431 (t0) cc_final: 0.6988 (t0) REVERT: E 739 THR cc_start: 0.8425 (m) cc_final: 0.8160 (p) REVERT: C 26 GLN cc_start: 0.7405 (tm-30) cc_final: 0.7129 (tm-30) REVERT: C 878 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7761 (mp) REVERT: C 950 ASP cc_start: 0.7711 (m-30) cc_final: 0.7451 (m-30) outliers start: 62 outliers final: 53 residues processed: 281 average time/residue: 0.3972 time to fit residues: 191.4582 Evaluate side-chains 284 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 227 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 515 PHE Chi-restraints excluded: chain E residue 660 TYR Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 826 VAL Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1100 THR Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 243 optimal weight: 2.9990 chunk 326 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 282 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 306 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 314 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.201392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.137981 restraints weight = 51034.043| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.13 r_work: 0.3514 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32173 Z= 0.169 Angle : 0.542 10.914 43805 Z= 0.272 Chirality : 0.043 0.253 5079 Planarity : 0.004 0.062 5595 Dihedral : 5.418 59.409 5580 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.65 % Favored : 92.30 % Rotamer: Outliers : 1.84 % Allowed : 13.81 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.90 (0.14), residues: 3871 helix: 1.48 (0.17), residues: 1005 sheet: -0.53 (0.20), residues: 636 loop : -1.68 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 271 HIS 0.006 0.001 HIS A 374 PHE 0.024 0.001 PHE D 543 TYR 0.019 0.001 TYR E 451 ARG 0.003 0.000 ARG E 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6873.18 seconds wall clock time: 126 minutes 59.14 seconds (7619.14 seconds total)