Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 14 23:48:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/07_2023/7yr2_34043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/07_2023/7yr2_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_34043/07_2023/7yr2_34043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/07_2023/7yr2_34043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/07_2023/7yr2_34043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr2_34043/07_2023/7yr2_34043.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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 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 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 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 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 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 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 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 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 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 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 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 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 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: 17.80, per 1000 atoms: 0.57 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: 12.09 Conformation dependent library (CDL) restraints added in 5.7 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: 1.85 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: 11.51 Time building geometry restraints manager: 13.13 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 - 17.98: 16771 17.98 - 35.95: 1467 35.95 - 53.93: 263 53.93 - 71.90: 53 71.90 - 89.88: 39 Dihedral angle restraints: 18593 sinusoidal: 7244 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 18590 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.130 Check model and map are aligned: 0.480 Set scattering table: 0.240 Process input model: 83.860 Find NCS groups from input model: 1.810 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.390 ------------------------------------------------------------------------------- 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 : 14.231 89.880 11182 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 % 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 *********************** 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 : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.3945 time to fit residues: 216.0855 Evaluate side-chains 222 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.307 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6774 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 32173 Z= 0.227 Angle : 0.592 11.000 43805 Z= 0.301 Chirality : 0.045 0.245 5079 Planarity : 0.004 0.059 5595 Dihedral : 4.370 30.590 4173 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.55 % Favored : 92.40 % Rotamer Outliers : 1.19 % 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: -1.17 (0.13), residues: 3871 helix: 1.04 (0.17), residues: 999 sheet: -0.67 (0.20), residues: 588 loop : -1.73 (0.13), residues: 2284 *********************** 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 300 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 28 residues processed: 287 average time/residue: 0.3786 time to fit residues: 186.1834 Evaluate side-chains 250 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 222 time to evaluate : 3.226 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2741 time to fit residues: 19.0427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 194 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 291 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 351 optimal weight: 3.9990 chunk 379 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 348 optimal weight: 0.3980 chunk 119 optimal weight: 7.9990 chunk 281 optimal weight: 0.4980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** E 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 ASN ** 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** C1071 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 32173 Z= 0.201 Angle : 0.572 13.662 43805 Z= 0.287 Chirality : 0.045 0.661 5079 Planarity : 0.004 0.058 5595 Dihedral : 4.286 28.576 4173 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.60 % Favored : 92.37 % Rotamer Outliers : 1.10 % 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: -1.10 (0.13), residues: 3871 helix: 1.17 (0.17), residues: 1006 sheet: -0.69 (0.20), residues: 576 loop : -1.70 (0.13), residues: 2289 *********************** 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 298 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 261 time to evaluate : 3.856 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 13 residues processed: 288 average time/residue: 0.3858 time to fit residues: 188.8599 Evaluate side-chains 251 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 238 time to evaluate : 3.374 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2851 time to fit residues: 11.5646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 182 optimal weight: 8.9990 chunk 38 optimal weight: 30.0000 chunk 167 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 352 optimal weight: 0.7980 chunk 373 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 334 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 607 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN C 183 GLN C 370 ASN C 394 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: 0.7267 moved from start: 0.1441 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= 0.197 Angle : 0.560 10.411 43805 Z= 0.281 Chirality : 0.044 0.573 5079 Planarity : 0.004 0.059 5595 Dihedral : 4.235 28.236 4173 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.76 % Favored : 92.22 % Rotamer Outliers : 1.01 % 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: -1.08 (0.13), residues: 3871 helix: 1.24 (0.17), residues: 1007 sheet: -0.72 (0.20), residues: 556 loop : -1.70 (0.13), residues: 2308 *********************** 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 290 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 256 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 277 average time/residue: 0.4089 time to fit residues: 190.5635 Evaluate side-chains 250 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 233 time to evaluate : 3.392 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2949 time to fit residues: 13.9998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 310 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 318 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 190 optimal weight: 7.9990 chunk 334 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 552 GLN ** D 394 ASN ** 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 542 ASN D 607 GLN E 52 GLN E 314 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 32173 Z= 0.213 Angle : 0.558 9.711 43805 Z= 0.281 Chirality : 0.044 0.327 5079 Planarity : 0.004 0.060 5595 Dihedral : 4.232 26.505 4173 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.73 % Favored : 92.24 % Rotamer Outliers : 0.83 % 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: 1.22 (0.17), residues: 1017 sheet: -0.68 (0.20), residues: 591 loop : -1.69 (0.13), residues: 2263 *********************** 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 278 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 250 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 264 average time/residue: 0.3987 time to fit residues: 180.6553 Evaluate side-chains 256 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 238 time to evaluate : 3.256 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3194 time to fit residues: 15.0088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 73 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 373 optimal weight: 0.6980 chunk 310 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 196 optimal weight: 0.0670 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** 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** E 613 GLN E 926 GLN C 394 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 32173 Z= 0.180 Angle : 0.549 9.801 43805 Z= 0.275 Chirality : 0.043 0.257 5079 Planarity : 0.004 0.061 5595 Dihedral : 4.142 26.144 4173 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.60 % Favored : 92.35 % Rotamer Outliers : 0.83 % 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: -0.97 (0.13), residues: 3871 helix: 1.38 (0.17), residues: 999 sheet: -0.63 (0.20), residues: 600 loop : -1.67 (0.13), residues: 2272 *********************** 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 283 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 255 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 278 average time/residue: 0.4006 time to fit residues: 190.8020 Evaluate side-chains 243 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 231 time to evaluate : 3.363 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2841 time to fit residues: 11.2009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 360 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 212 optimal weight: 0.5980 chunk 272 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 314 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 372 optimal weight: 0.8980 chunk 232 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 394 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1905 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= 0.175 Angle : 0.550 10.343 43805 Z= 0.276 Chirality : 0.044 0.574 5079 Planarity : 0.004 0.061 5595 Dihedral : 4.134 31.987 4173 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.57 % Favored : 92.37 % Rotamer Outliers : 0.68 % 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: -0.91 (0.13), residues: 3871 helix: 1.49 (0.17), residues: 987 sheet: -0.59 (0.20), residues: 602 loop : -1.65 (0.13), residues: 2282 *********************** 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 272 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 249 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 6 residues processed: 268 average time/residue: 0.3993 time to fit residues: 181.3942 Evaluate side-chains 243 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 237 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2829 time to fit residues: 7.8798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 230 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 chunk 222 optimal weight: 7.9990 chunk 112 optimal weight: 0.0570 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 236 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 292 optimal weight: 0.0970 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 542 ASN D 607 GLN C 394 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1994 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= 0.149 Angle : 0.539 10.497 43805 Z= 0.271 Chirality : 0.043 0.335 5079 Planarity : 0.004 0.062 5595 Dihedral : 4.032 28.445 4173 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.21 % Favored : 92.74 % Rotamer Outliers : 0.53 % 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: -0.86 (0.14), residues: 3871 helix: 1.50 (0.17), residues: 999 sheet: -0.51 (0.20), residues: 609 loop : -1.63 (0.13), residues: 2263 *********************** 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 274 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 256 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 268 average time/residue: 0.4058 time to fit residues: 185.6886 Evaluate side-chains 244 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 233 time to evaluate : 3.353 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2987 time to fit residues: 10.8561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 338 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 chunk 325 optimal weight: 0.0570 chunk 346 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 313 optimal weight: 0.9980 chunk 327 optimal weight: 7.9990 chunk 345 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 542 ASN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 32173 Z= 0.185 Angle : 0.550 10.535 43805 Z= 0.275 Chirality : 0.044 0.297 5079 Planarity : 0.004 0.062 5595 Dihedral : 4.059 28.141 4173 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.26 % Favored : 92.68 % Rotamer Outliers : 0.24 % 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: 1.43 (0.17), residues: 1005 sheet: -0.58 (0.20), residues: 620 loop : -1.63 (0.13), residues: 2246 *********************** 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 246 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 238 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 243 average time/residue: 0.4075 time to fit residues: 168.9837 Evaluate side-chains 234 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 226 time to evaluate : 3.468 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3351 time to fit residues: 10.0368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 227 optimal weight: 0.0050 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 254 optimal weight: 0.5980 chunk 384 optimal weight: 0.6980 chunk 353 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 236 optimal weight: 0.7980 chunk 187 optimal weight: 0.3980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 542 ASN D 607 GLN C 115 GLN C 394 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 32173 Z= 0.152 Angle : 0.542 10.684 43805 Z= 0.272 Chirality : 0.043 0.265 5079 Planarity : 0.004 0.062 5595 Dihedral : 3.981 27.234 4173 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.98 % Favored : 92.99 % Rotamer Outliers : 0.18 % 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: -0.85 (0.14), residues: 3871 helix: 1.46 (0.17), residues: 1011 sheet: -0.41 (0.20), residues: 621 loop : -1.65 (0.13), residues: 2239 ********************** 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 251 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 245 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 249 average time/residue: 0.4231 time to fit residues: 179.8252 Evaluate side-chains 229 residues out of total 3400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 3.428 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3214 time to fit residues: 6.6650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 243 optimal weight: 0.9990 chunk 326 optimal weight: 4.9990 chunk 93 optimal weight: 0.0020 chunk 282 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- 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 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN D 542 ASN D 607 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.193389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131319 restraints weight = 50940.331| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.95 r_work: 0.3417 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 32173 Z= 0.291 Angle : 0.602 10.397 43805 Z= 0.302 Chirality : 0.045 0.260 5079 Planarity : 0.004 0.061 5595 Dihedral : 4.299 29.487 4173 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.12 % Favored : 91.86 % Rotamer Outliers : 0.24 % 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: -1.02 (0.13), residues: 3871 helix: 1.30 (0.17), residues: 995 sheet: -0.68 (0.20), residues: 628 loop : -1.67 (0.13), residues: 2248 =============================================================================== Job complete usr+sys time: 6380.61 seconds wall clock time: 117 minutes 6.14 seconds (7026.14 seconds total)