Starting phenix.real_space_refine on Fri Sep 19 14:16:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jw0_22512/09_2025/7jw0_22512.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jw0_22512/09_2025/7jw0_22512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jw0_22512/09_2025/7jw0_22512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jw0_22512/09_2025/7jw0_22512.map" model { file = "/net/cci-nas-00/data/ceres_data/7jw0_22512/09_2025/7jw0_22512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jw0_22512/09_2025/7jw0_22512.cif" } resolution = 4.3 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 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= 0.004 sd= 0.044 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: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 16324 2.51 5 N 4778 2.21 5 O 5026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26251 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 6270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 6270 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 533} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 9 Unresolved non-hydrogen bonds: 1641 Unresolved non-hydrogen angles: 2121 Unresolved non-hydrogen dihedrals: 1250 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'ARG:plan': 18, 'GLN:plan1': 30, 'ASN:plan1': 48, 'ASP:plan': 42, 'PHE:plan': 21, 'HIS:plan': 4, 'GLU:plan': 34, 'TYR:plan': 13} Unresolved non-hydrogen planarities: 853 Chain: "L" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1074 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 199} Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 14, 'ASP:plan': 9, 'ARG:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 6, 'TRP:plan': 2, 'PHE:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "H" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1097 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 750 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 5, 'ARG:plan': 6, 'PHE:plan': 7, 'TYR:plan': 14, 'ASP:plan': 9, 'HIS:plan': 3, 'TRP:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 314 Chain: "B" Number of atoms: 6237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 6237 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 539} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1681 Unresolved non-hydrogen angles: 2176 Unresolved non-hydrogen dihedrals: 1292 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'ARG:plan': 18, 'GLN:plan1': 30, 'ASN:plan1': 48, 'ASP:plan': 42, 'PHE:plan': 22, 'HIS:plan': 4, 'GLU:plan': 34, 'TYR:plan': 15, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 882 Chain: "C" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1074 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 199} Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 14, 'ASP:plan': 9, 'ARG:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 6, 'TRP:plan': 2, 'PHE:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "D" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1097 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 750 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 5, 'ARG:plan': 6, 'PHE:plan': 7, 'TYR:plan': 14, 'ASP:plan': 9, 'HIS:plan': 3, 'TRP:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 314 Chain: "E" Number of atoms: 6271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 6271 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 532} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 9 Unresolved non-hydrogen bonds: 1640 Unresolved non-hydrogen angles: 2120 Unresolved non-hydrogen dihedrals: 1249 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'ARG:plan': 18, 'GLN:plan1': 30, 'ASN:plan1': 48, 'ASP:plan': 42, 'PHE:plan': 21, 'HIS:plan': 4, 'GLU:plan': 34, 'TYR:plan': 13} Unresolved non-hydrogen planarities: 853 Chain: "F" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1077 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 199} Unresolved non-hydrogen bonds: 567 Unresolved non-hydrogen angles: 727 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 14, 'ASP:plan': 9, 'ARG:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 6, 'TRP:plan': 2, 'PHE:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 316 Chain: "G" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1097 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 750 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 5, 'ARG:plan': 6, 'PHE:plan': 7, 'TYR:plan': 14, 'ASP:plan': 9, 'HIS:plan': 3, 'TRP:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 314 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 7.60, per 1000 atoms: 0.29 Number of scatterers: 26251 At special positions: 0 Unit cell: (147, 152.25, 203.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 5026 8.00 N 4778 7.00 C 16324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.87 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.08 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.02 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.87 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.02 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=1.87 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.08 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 538 " - pdb=" SG CYS E 590 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.04 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.02 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 717 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E 717 " " NAG E1311 " - " ASN E1074 " " NAG E1312 " - " ASN E 165 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 343 " " NAG N 1 " - " ASN A 17 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 17 " " NAG T 1 " - " ASN E 801 " " NAG U 1 " - " ASN E1098 " " NAG V 1 " - " ASN E1134 " " NAG W 1 " - " ASN E 343 " " NAG X 1 " - " ASN E 17 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 nanoseconds 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8040 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 87 sheets defined 20.9% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.946A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.345A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.707A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.219A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 941 through 944 removed outlier: 4.052A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.826A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.989A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.178A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 185 through 187 No H-bonds generated for 'chain 'L' and resid 185 through 187' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 211 No H-bonds generated for 'chain 'H' and resid 209 through 211' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.945A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.345A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.706A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.219A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 removed outlier: 4.053A pdb=" N ALA B 944 " --> pdb=" O THR B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.826A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.989A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.178A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 185 through 187 No H-bonds generated for 'chain 'C' and resid 185 through 187' Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 383 through 388 removed outlier: 3.945A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.345A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.706A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.219A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 939 Processing helix chain 'E' and resid 941 through 944 removed outlier: 4.053A pdb=" N ALA E 944 " --> pdb=" O THR E 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 941 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.826A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 982 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.989A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1147 removed outlier: 4.178A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'G' and resid 134 through 136 No H-bonds generated for 'chain 'G' and resid 134 through 136' Processing helix chain 'G' and resid 163 through 165 No H-bonds generated for 'chain 'G' and resid 163 through 165' Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.056A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.543A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.895A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 140 removed outlier: 5.592A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.276A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.994A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.478A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.478A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.669A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.435A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.449A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.899A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.941A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.526A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.554A pdb=" N ALA L 84 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.554A pdb=" N ALA L 84 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.584A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.900A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.942A pdb=" N CYS H 95 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP H 110 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG H 97 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 127 through 131 removed outlier: 4.821A pdb=" N ALA H 144 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL H 191 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY H 146 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL H 189 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 138 through 139 removed outlier: 4.821A pdb=" N ALA H 144 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL H 191 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY H 146 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL H 189 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 157 through 161 removed outlier: 4.651A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.057A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.895A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'B' and resid 133 through 140 removed outlier: 5.591A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.277A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.995A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE B 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.478A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.478A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AF1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.669A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.435A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.449A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.941A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.527A pdb=" N SER C 67 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.555A pdb=" N ALA C 84 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.555A pdb=" N ALA C 84 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR C 98 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 115 through 119 removed outlier: 4.584A pdb=" N SER C 132 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU C 182 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL C 134 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU C 180 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU C 136 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER C 178 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN C 138 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU C 176 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AG1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.899A pdb=" N MET D 34 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.941A pdb=" N CYS D 95 " --> pdb=" O TRP D 110 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP D 110 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG D 97 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 127 through 131 removed outlier: 4.822A pdb=" N ALA D 144 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL D 191 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY D 146 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 189 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU D 148 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER D 187 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS D 150 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 185 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 138 through 139 removed outlier: 4.822A pdb=" N ALA D 144 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL D 191 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY D 146 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 189 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU D 148 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER D 187 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS D 150 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 185 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 157 through 161 removed outlier: 4.651A pdb=" N TYR D 201 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 27 through 30 removed outlier: 8.056A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.895A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG E 273 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 83 through 85 Processing sheet with id=AH1, first strand: chain 'E' and resid 133 through 140 removed outlier: 5.591A pdb=" N GLN E 134 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL E 159 " --> pdb=" O CYS E 136 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.277A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 325 through 328 Processing sheet with id=AH4, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AH7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AH8, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.477A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR E 660 " --> pdb=" O SER E 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.477A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.669A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 718 through 728 removed outlier: 7.435A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.449A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.941A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.527A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.555A pdb=" N ALA F 84 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.555A pdb=" N ALA F 84 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.585A pdb=" N SER F 132 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU F 182 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL F 134 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU F 180 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU F 136 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER F 178 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN F 138 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU F 176 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AJ1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AJ2, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.900A pdb=" N MET G 34 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.941A pdb=" N CYS G 95 " --> pdb=" O TRP G 110 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP G 110 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG G 97 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'G' and resid 127 through 131 removed outlier: 4.821A pdb=" N ALA G 144 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL G 191 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY G 146 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL G 189 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU G 148 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER G 187 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS G 150 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU G 185 " --> pdb=" O LYS G 150 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'G' and resid 138 through 139 removed outlier: 4.821A pdb=" N ALA G 144 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL G 191 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY G 146 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL G 189 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU G 148 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER G 187 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS G 150 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU G 185 " --> pdb=" O LYS G 150 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'G' and resid 157 through 161 removed outlier: 4.651A pdb=" N TYR G 201 " --> pdb=" O VAL G 218 " (cutoff:3.500A) 1439 hydrogen bonds defined for protein. 3759 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: 10.83 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7609 1.33 - 1.46: 6954 1.46 - 1.59: 12005 1.59 - 1.72: 3 1.72 - 1.85: 141 Bond restraints: 26712 Sorted by residual: bond pdb=" C ASN E 81 " pdb=" N PRO E 82 " ideal model delta sigma weight residual 1.328 1.381 -0.053 1.26e-02 6.30e+03 1.75e+01 bond pdb=" C ASN B 81 " pdb=" N PRO B 82 " ideal model delta sigma weight residual 1.328 1.381 -0.052 1.26e-02 6.30e+03 1.72e+01 bond pdb=" C ASN A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.328 1.380 -0.052 1.26e-02 6.30e+03 1.71e+01 bond pdb=" N PRO G 220 " pdb=" CD PRO G 220 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" N PRO H 220 " pdb=" CD PRO H 220 " ideal model delta sigma weight residual 1.473 1.523 -0.050 1.40e-02 5.10e+03 1.29e+01 ... (remaining 26707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.78: 36843 6.78 - 13.57: 50 13.57 - 20.35: 3 20.35 - 27.13: 0 27.13 - 33.92: 3 Bond angle restraints: 36899 Sorted by residual: angle pdb=" N SER A 939 " pdb=" CA SER A 939 " pdb=" C SER A 939 " ideal model delta sigma weight residual 111.37 145.29 -33.92 1.65e+00 3.67e-01 4.23e+02 angle pdb=" N SER E 939 " pdb=" CA SER E 939 " pdb=" C SER E 939 " ideal model delta sigma weight residual 111.37 145.27 -33.90 1.65e+00 3.67e-01 4.22e+02 angle pdb=" N SER B 939 " pdb=" CA SER B 939 " pdb=" C SER B 939 " ideal model delta sigma weight residual 111.37 145.23 -33.86 1.65e+00 3.67e-01 4.21e+02 angle pdb=" N SER A 940 " pdb=" CA SER A 940 " pdb=" CB SER A 940 " ideal model delta sigma weight residual 110.81 91.69 19.12 1.48e+00 4.57e-01 1.67e+02 angle pdb=" N SER B 940 " pdb=" CA SER B 940 " pdb=" CB SER B 940 " ideal model delta sigma weight residual 110.81 91.71 19.10 1.48e+00 4.57e-01 1.67e+02 ... (remaining 36894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 16260 21.31 - 42.62: 248 42.62 - 63.93: 27 63.93 - 85.24: 30 85.24 - 106.55: 21 Dihedral angle restraints: 16586 sinusoidal: 4177 harmonic: 12409 Sorted by residual: dihedral pdb=" N SER E 939 " pdb=" C SER E 939 " pdb=" CA SER E 939 " pdb=" CB SER E 939 " ideal model delta harmonic sigma weight residual 122.80 156.52 -33.72 0 2.50e+00 1.60e-01 1.82e+02 dihedral pdb=" N SER A 939 " pdb=" C SER A 939 " pdb=" CA SER A 939 " pdb=" CB SER A 939 " ideal model delta harmonic sigma weight residual 122.80 156.52 -33.72 0 2.50e+00 1.60e-01 1.82e+02 dihedral pdb=" N SER B 939 " pdb=" C SER B 939 " pdb=" CA SER B 939 " pdb=" CB SER B 939 " ideal model delta harmonic sigma weight residual 122.80 156.49 -33.69 0 2.50e+00 1.60e-01 1.82e+02 ... (remaining 16583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.353: 4615 0.353 - 0.705: 6 0.705 - 1.058: 0 1.058 - 1.410: 0 1.410 - 1.763: 3 Chirality restraints: 4624 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.70e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.61e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.39e+01 ... (remaining 4621 not shown) Planarity restraints: 5097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.051 2.00e-02 2.50e+03 5.18e-02 3.36e+01 pdb=" CG ASN A1074 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.079 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E1074 " 0.050 2.00e-02 2.50e+03 5.17e-02 3.34e+01 pdb=" CG ASN E1074 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN E1074 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN E1074 " -0.079 2.00e-02 2.50e+03 pdb=" C1 NAG E1311 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " -0.050 2.00e-02 2.50e+03 5.17e-02 3.33e+01 pdb=" CG ASN B1074 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " 0.078 2.00e-02 2.50e+03 pdb=" C1 NAG B1311 " -0.063 2.00e-02 2.50e+03 ... (remaining 5094 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 13594 3.00 - 3.48: 23236 3.48 - 3.95: 36890 3.95 - 4.43: 39025 4.43 - 4.90: 65328 Nonbonded interactions: 178073 Sorted by model distance: nonbonded pdb=" N PRO A 600 " pdb=" O PRO A 600 " model vdw 2.527 2.496 nonbonded pdb=" N PRO E 600 " pdb=" O PRO E 600 " model vdw 2.527 2.496 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.527 2.496 nonbonded pdb=" N GLY E1085 " pdb=" N LYS E1086 " model vdw 2.551 2.560 nonbonded pdb=" N GLY B1085 " pdb=" N LYS B1086 " model vdw 2.551 2.560 ... (remaining 178068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 422 or (resid 423 through 430 and (name N or na \ me CA or name C or name O or name CB )) or resid 431 or (resid 432 through 444 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 447 through 47 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 476 through \ 1075 or (resid 1076 through 1078 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1079 through 1312)) selection = (chain 'B' and (resid 15 through 365 or (resid 366 through 373 and (name N or na \ me CA or name C or name O or name CB )) or resid 374 through 1075 or (resid 1076 \ through 1078 and (name N or name CA or name C or name O or name CB )) or resid \ 1079 through 1312)) selection = (chain 'E' and (resid 15 through 365 or (resid 366 through 373 and (name N or na \ me CA or name C or name O or name CB )) or resid 374 through 422 or (resid 423 t \ hrough 430 and (name N or name CA or name C or name O or name CB )) or resid 431 \ or (resid 432 through 444 and (name N or name CA or name C or name O or name CB \ )) or (resid 447 through 475 and (name N or name CA or name C or name O or name \ CB )) or resid 476 through 1076 or (resid 1077 through 1078 and (name N or name \ CA or name C or name O or name CB )) or resid 1079 through 1312)) } ncs_group { reference = chain 'C' selection = (chain 'F' and (resid 2 through 102 or (resid 103 through 113 and (name N or nam \ e CA or name C or name O or name CB )) or resid 114 through 194 or (resid 195 th \ rough 200 and (name N or name CA or name C or name O or name CB )) or resid 201 \ through 213)) selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'M' selection = chain 'R' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.250 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 34.060 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 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 : 0.011 0.164 26832 Z= 0.637 Angle : 1.548 33.916 37208 Z= 1.034 Chirality : 0.098 1.763 4624 Planarity : 0.005 0.024 5046 Dihedral : 9.597 106.547 8393 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.33 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.12), residues: 4242 helix: -0.01 (0.17), residues: 714 sheet: 1.45 (0.14), residues: 1218 loop : 0.65 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 355 TYR 0.029 0.005 TYR A 495 PHE 0.022 0.003 PHE B 898 TRP 0.022 0.006 TRP B1102 HIS 0.006 0.001 HIS E1083 Details of bonding type rmsd covalent geometry : bond 0.01040 (26712) covalent geometry : angle 1.53534 (36899) SS BOND : bond 0.04116 ( 51) SS BOND : angle 2.96674 ( 102) hydrogen bonds : bond 0.16627 ( 1400) hydrogen bonds : angle 8.15565 ( 3759) link_BETA1-4 : bond 0.05671 ( 18) link_BETA1-4 : angle 2.90614 ( 54) link_NAG-ASN : bond 0.05779 ( 51) link_NAG-ASN : angle 2.30033 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 707 TYR cc_start: 0.7400 (t80) cc_final: 0.7058 (t80) REVERT: A 1064 HIS cc_start: 0.8172 (m-70) cc_final: 0.7848 (m170) REVERT: A 1095 PHE cc_start: 0.8060 (m-80) cc_final: 0.7547 (m-10) REVERT: B 900 MET cc_start: 0.8596 (mmm) cc_final: 0.8171 (tpp) REVERT: B 1039 ARG cc_start: 0.7479 (mtp180) cc_final: 0.7242 (mmm-85) REVERT: B 1064 HIS cc_start: 0.8379 (m-70) cc_final: 0.8117 (m170) REVERT: B 1095 PHE cc_start: 0.7991 (m-80) cc_final: 0.7486 (m-10) REVERT: E 900 MET cc_start: 0.8679 (mmm) cc_final: 0.8084 (tpp) REVERT: E 1021 SER cc_start: 0.9545 (m) cc_final: 0.9287 (p) REVERT: E 1039 ARG cc_start: 0.7618 (mtp180) cc_final: 0.7339 (mmm-85) REVERT: E 1095 PHE cc_start: 0.7904 (m-80) cc_final: 0.7616 (m-10) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1482 time to fit residues: 68.8671 Evaluate side-chains 122 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 50.0000 chunk 424 optimal weight: 0.0980 chunk 155 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1048 HIS ** E1083 HIS ** 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 = 0.3899 r_free = 0.3899 target = 0.106756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.085848 restraints weight = 118495.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085309 restraints weight = 111642.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.085886 restraints weight = 95675.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086050 restraints weight = 80373.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.086302 restraints weight = 68653.353| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 26832 Z= 0.165 Angle : 0.614 8.820 37208 Z= 0.324 Chirality : 0.048 0.391 4624 Planarity : 0.004 0.039 5046 Dihedral : 6.275 63.176 5860 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.53 % Favored : 98.40 % Rotamer: Outliers : 0.26 % Allowed : 2.27 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.13), residues: 4242 helix: 1.70 (0.20), residues: 684 sheet: 1.40 (0.14), residues: 1236 loop : 0.55 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.015 0.002 TYR B 707 PHE 0.029 0.002 PHE A1052 TRP 0.011 0.001 TRP A 886 HIS 0.005 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00339 (26712) covalent geometry : angle 0.58297 (36899) SS BOND : bond 0.00465 ( 51) SS BOND : angle 1.81726 ( 102) hydrogen bonds : bond 0.04106 ( 1400) hydrogen bonds : angle 6.04837 ( 3759) link_BETA1-4 : bond 0.00448 ( 18) link_BETA1-4 : angle 1.96874 ( 54) link_NAG-ASN : bond 0.00478 ( 51) link_NAG-ASN : angle 2.49608 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 183 time to evaluate : 0.624 Fit side-chains REVERT: A 707 TYR cc_start: 0.7629 (t80) cc_final: 0.7051 (t80) REVERT: A 1050 MET cc_start: 0.7936 (ptm) cc_final: 0.7295 (ptm) REVERT: A 1064 HIS cc_start: 0.8370 (m-70) cc_final: 0.7842 (m170) REVERT: A 1072 GLU cc_start: 0.8898 (pm20) cc_final: 0.8664 (pm20) REVERT: B 318 PHE cc_start: 0.7364 (t80) cc_final: 0.7110 (t80) REVERT: B 707 TYR cc_start: 0.7331 (t80) cc_final: 0.7095 (t80) REVERT: B 900 MET cc_start: 0.8613 (mmm) cc_final: 0.7918 (tpp) REVERT: B 1039 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7432 (mtm-85) REVERT: B 1064 HIS cc_start: 0.8360 (m-70) cc_final: 0.7942 (m170) REVERT: B 1095 PHE cc_start: 0.8365 (m-80) cc_final: 0.8093 (m-80) REVERT: B 1139 ASP cc_start: 0.8434 (t0) cc_final: 0.8220 (t0) REVERT: E 900 MET cc_start: 0.8322 (mmm) cc_final: 0.8094 (tpp) REVERT: E 1064 HIS cc_start: 0.8279 (m170) cc_final: 0.7994 (m170) REVERT: E 1072 GLU cc_start: 0.9024 (pm20) cc_final: 0.8574 (pm20) REVERT: E 1095 PHE cc_start: 0.8300 (m-80) cc_final: 0.8021 (m-10) REVERT: E 1139 ASP cc_start: 0.8323 (t0) cc_final: 0.8121 (t0) outliers start: 3 outliers final: 0 residues processed: 186 average time/residue: 0.1433 time to fit residues: 45.1569 Evaluate side-chains 105 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 248 optimal weight: 30.0000 chunk 115 optimal weight: 40.0000 chunk 139 optimal weight: 40.0000 chunk 203 optimal weight: 0.9980 chunk 325 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 418 optimal weight: 5.9990 chunk 357 optimal weight: 0.8980 chunk 288 optimal weight: 0.9980 chunk 187 optimal weight: 30.0000 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.099956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.077623 restraints weight = 117183.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.075989 restraints weight = 97089.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076757 restraints weight = 106716.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076723 restraints weight = 84633.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077043 restraints weight = 75500.881| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 26832 Z= 0.288 Angle : 0.690 10.217 37208 Z= 0.369 Chirality : 0.048 0.324 4624 Planarity : 0.005 0.071 5046 Dihedral : 5.509 46.700 5860 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.13), residues: 4242 helix: 1.35 (0.19), residues: 681 sheet: 1.04 (0.14), residues: 1302 loop : 0.32 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1014 TYR 0.025 0.003 TYR B 380 PHE 0.052 0.003 PHE A 906 TRP 0.016 0.002 TRP A 886 HIS 0.022 0.003 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00614 (26712) covalent geometry : angle 0.66315 (36899) SS BOND : bond 0.01102 ( 51) SS BOND : angle 1.98072 ( 102) hydrogen bonds : bond 0.05143 ( 1400) hydrogen bonds : angle 6.14542 ( 3759) link_BETA1-4 : bond 0.00330 ( 18) link_BETA1-4 : angle 1.53488 ( 54) link_NAG-ASN : bond 0.00447 ( 51) link_NAG-ASN : angle 2.47492 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.921 Fit side-chains REVERT: A 781 VAL cc_start: 0.9406 (t) cc_final: 0.8964 (p) REVERT: A 1139 ASP cc_start: 0.8497 (t70) cc_final: 0.8227 (t0) REVERT: B 318 PHE cc_start: 0.7612 (t80) cc_final: 0.7400 (t80) REVERT: B 707 TYR cc_start: 0.7978 (t80) cc_final: 0.7306 (t80) REVERT: B 781 VAL cc_start: 0.9339 (t) cc_final: 0.8937 (p) REVERT: B 900 MET cc_start: 0.8287 (mmm) cc_final: 0.7829 (tpp) REVERT: B 1139 ASP cc_start: 0.8666 (t0) cc_final: 0.8354 (t0) REVERT: E 731 MET cc_start: 0.8486 (ttp) cc_final: 0.8240 (ttm) REVERT: E 782 PHE cc_start: 0.8792 (m-80) cc_final: 0.8579 (m-10) REVERT: E 1064 HIS cc_start: 0.8418 (m170) cc_final: 0.7971 (m170) REVERT: E 1139 ASP cc_start: 0.8658 (t0) cc_final: 0.8369 (t0) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.1436 time to fit residues: 31.5730 Evaluate side-chains 85 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 396 optimal weight: 50.0000 chunk 361 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 421 optimal weight: 30.0000 chunk 283 optimal weight: 5.9990 chunk 249 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 266 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 GLN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.096648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.073673 restraints weight = 118060.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.071683 restraints weight = 102150.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.072365 restraints weight = 103930.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072520 restraints weight = 81569.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072678 restraints weight = 76674.898| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 26832 Z= 0.368 Angle : 0.762 12.053 37208 Z= 0.404 Chirality : 0.050 0.329 4624 Planarity : 0.006 0.082 5046 Dihedral : 5.834 39.854 5860 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.26 % Allowed : 4.55 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.13), residues: 4242 helix: 0.90 (0.19), residues: 687 sheet: 0.66 (0.14), residues: 1293 loop : -0.07 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 355 TYR 0.032 0.003 TYR A 707 PHE 0.050 0.004 PHE E 192 TRP 0.018 0.002 TRP A 886 HIS 0.008 0.003 HIS E1083 Details of bonding type rmsd covalent geometry : bond 0.00780 (26712) covalent geometry : angle 0.72825 (36899) SS BOND : bond 0.00750 ( 51) SS BOND : angle 2.51222 ( 102) hydrogen bonds : bond 0.05364 ( 1400) hydrogen bonds : angle 6.44383 ( 3759) link_BETA1-4 : bond 0.00192 ( 18) link_BETA1-4 : angle 1.51837 ( 54) link_NAG-ASN : bond 0.00871 ( 51) link_NAG-ASN : angle 2.85927 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.000 Fit side-chains REVERT: A 275 PHE cc_start: 0.8729 (m-80) cc_final: 0.8520 (m-80) REVERT: A 365 TYR cc_start: 0.8430 (m-10) cc_final: 0.8185 (m-10) REVERT: A 1072 GLU cc_start: 0.9118 (pm20) cc_final: 0.8595 (pm20) REVERT: A 1139 ASP cc_start: 0.8597 (t70) cc_final: 0.8329 (t0) REVERT: B 271 GLN cc_start: 0.8425 (mp10) cc_final: 0.8219 (mp10) REVERT: B 707 TYR cc_start: 0.8333 (t80) cc_final: 0.8101 (t80) REVERT: B 900 MET cc_start: 0.8235 (mmm) cc_final: 0.7904 (tpp) REVERT: B 1072 GLU cc_start: 0.9020 (pm20) cc_final: 0.8358 (pm20) REVERT: B 1139 ASP cc_start: 0.8723 (t0) cc_final: 0.8411 (t0) REVERT: E 731 MET cc_start: 0.8463 (ttp) cc_final: 0.8224 (ttm) REVERT: E 1064 HIS cc_start: 0.8444 (m170) cc_final: 0.7949 (m170) REVERT: E 1072 GLU cc_start: 0.9039 (pm20) cc_final: 0.8696 (pm20) REVERT: E 1083 HIS cc_start: 0.8530 (t-90) cc_final: 0.8130 (t70) REVERT: E 1139 ASP cc_start: 0.8804 (t0) cc_final: 0.8460 (t0) outliers start: 3 outliers final: 0 residues processed: 107 average time/residue: 0.1320 time to fit residues: 25.6877 Evaluate side-chains 87 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 228 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 302 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 248 optimal weight: 40.0000 chunk 382 optimal weight: 10.0000 chunk 411 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.098091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.075770 restraints weight = 116877.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073700 restraints weight = 99981.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074373 restraints weight = 103459.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074637 restraints weight = 77991.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074847 restraints weight = 71922.171| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26832 Z= 0.188 Angle : 0.584 7.736 37208 Z= 0.305 Chirality : 0.047 0.286 4624 Planarity : 0.004 0.056 5046 Dihedral : 5.234 44.565 5860 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.13), residues: 4242 helix: 1.47 (0.20), residues: 684 sheet: 0.48 (0.14), residues: 1314 loop : 0.00 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.022 0.002 TYR A 707 PHE 0.022 0.002 PHE B 906 TRP 0.015 0.001 TRP B 104 HIS 0.007 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00395 (26712) covalent geometry : angle 0.55769 (36899) SS BOND : bond 0.00538 ( 51) SS BOND : angle 1.59067 ( 102) hydrogen bonds : bond 0.03931 ( 1400) hydrogen bonds : angle 5.84220 ( 3759) link_BETA1-4 : bond 0.00368 ( 18) link_BETA1-4 : angle 1.15786 ( 54) link_NAG-ASN : bond 0.00424 ( 51) link_NAG-ASN : angle 2.42521 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.957 Fit side-chains REVERT: A 365 TYR cc_start: 0.8400 (m-10) cc_final: 0.8164 (m-10) REVERT: A 900 MET cc_start: 0.7732 (mmt) cc_final: 0.7349 (mmt) REVERT: A 1072 GLU cc_start: 0.9108 (pm20) cc_final: 0.8581 (pm20) REVERT: A 1083 HIS cc_start: 0.8510 (t-90) cc_final: 0.8279 (t-90) REVERT: A 1139 ASP cc_start: 0.8538 (t70) cc_final: 0.8323 (t0) REVERT: B 271 GLN cc_start: 0.8268 (mp10) cc_final: 0.7992 (mp10) REVERT: B 365 TYR cc_start: 0.8384 (m-10) cc_final: 0.8170 (m-10) REVERT: B 707 TYR cc_start: 0.8069 (t80) cc_final: 0.7769 (t80) REVERT: B 1072 GLU cc_start: 0.8976 (pm20) cc_final: 0.8361 (pm20) REVERT: B 1139 ASP cc_start: 0.8762 (t0) cc_final: 0.8449 (t0) REVERT: E 781 VAL cc_start: 0.9303 (t) cc_final: 0.8904 (p) REVERT: E 900 MET cc_start: 0.8140 (mmt) cc_final: 0.7388 (mmm) REVERT: E 1064 HIS cc_start: 0.8367 (m170) cc_final: 0.7872 (m170) REVERT: E 1072 GLU cc_start: 0.9023 (pm20) cc_final: 0.8639 (pm20) REVERT: E 1139 ASP cc_start: 0.8837 (t0) cc_final: 0.8509 (t0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1387 time to fit residues: 28.9893 Evaluate side-chains 89 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 37 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 383 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 139 optimal weight: 40.0000 chunk 416 optimal weight: 50.0000 chunk 289 optimal weight: 4.9990 chunk 353 optimal weight: 1.9990 chunk 271 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 379 optimal weight: 0.3980 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.096590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074426 restraints weight = 117882.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072655 restraints weight = 101980.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073394 restraints weight = 115458.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073432 restraints weight = 86220.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073961 restraints weight = 76163.812| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26832 Z= 0.265 Angle : 0.643 8.610 37208 Z= 0.339 Chirality : 0.047 0.294 4624 Planarity : 0.005 0.065 5046 Dihedral : 5.375 46.158 5860 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.13), residues: 4242 helix: 1.20 (0.20), residues: 705 sheet: 0.36 (0.14), residues: 1356 loop : -0.17 (0.14), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 355 TYR 0.019 0.002 TYR B1047 PHE 0.043 0.002 PHE A 906 TRP 0.024 0.002 TRP B 886 HIS 0.005 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00562 (26712) covalent geometry : angle 0.61730 (36899) SS BOND : bond 0.00525 ( 51) SS BOND : angle 1.80438 ( 102) hydrogen bonds : bond 0.04488 ( 1400) hydrogen bonds : angle 5.92891 ( 3759) link_BETA1-4 : bond 0.00262 ( 18) link_BETA1-4 : angle 1.26439 ( 54) link_NAG-ASN : bond 0.00492 ( 51) link_NAG-ASN : angle 2.44950 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.951 Fit side-chains REVERT: A 365 TYR cc_start: 0.8368 (m-10) cc_final: 0.8055 (m-10) REVERT: A 1072 GLU cc_start: 0.9158 (pm20) cc_final: 0.8587 (pm20) REVERT: A 1083 HIS cc_start: 0.8536 (t-90) cc_final: 0.8296 (t-90) REVERT: A 1139 ASP cc_start: 0.8602 (t70) cc_final: 0.8394 (t0) REVERT: B 271 GLN cc_start: 0.8392 (mp10) cc_final: 0.8126 (mp10) REVERT: B 365 TYR cc_start: 0.8402 (m-10) cc_final: 0.8119 (m-10) REVERT: B 1017 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 1072 GLU cc_start: 0.9024 (pm20) cc_final: 0.8323 (pm20) REVERT: B 1139 ASP cc_start: 0.8781 (t0) cc_final: 0.8496 (t0) REVERT: E 900 MET cc_start: 0.7952 (mmt) cc_final: 0.7655 (mmt) REVERT: E 1050 MET cc_start: 0.8194 (ppp) cc_final: 0.7822 (ppp) REVERT: E 1064 HIS cc_start: 0.8368 (m170) cc_final: 0.7954 (m170) REVERT: E 1072 GLU cc_start: 0.8988 (pm20) cc_final: 0.8558 (pm20) REVERT: E 1083 HIS cc_start: 0.8385 (t-90) cc_final: 0.8129 (t-90) REVERT: E 1139 ASP cc_start: 0.8832 (t0) cc_final: 0.8519 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1342 time to fit residues: 27.3302 Evaluate side-chains 88 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 310 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 418 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 304 optimal weight: 0.4980 chunk 424 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.098175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075871 restraints weight = 117001.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074156 restraints weight = 101836.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.074722 restraints weight = 102546.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075073 restraints weight = 77660.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.075154 restraints weight = 70485.409| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26832 Z= 0.145 Angle : 0.538 7.240 37208 Z= 0.280 Chirality : 0.046 0.272 4624 Planarity : 0.004 0.051 5046 Dihedral : 4.918 43.371 5860 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.13), residues: 4242 helix: 1.82 (0.21), residues: 669 sheet: 0.34 (0.14), residues: 1338 loop : -0.06 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 905 TYR 0.013 0.001 TYR A 313 PHE 0.019 0.001 PHE B 906 TRP 0.017 0.001 TRP B 886 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00306 (26712) covalent geometry : angle 0.51416 (36899) SS BOND : bond 0.00325 ( 51) SS BOND : angle 1.43300 ( 102) hydrogen bonds : bond 0.03476 ( 1400) hydrogen bonds : angle 5.48465 ( 3759) link_BETA1-4 : bond 0.00385 ( 18) link_BETA1-4 : angle 1.07025 ( 54) link_NAG-ASN : bond 0.00305 ( 51) link_NAG-ASN : angle 2.20602 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8350 (m-10) cc_final: 0.8056 (m-10) REVERT: A 1072 GLU cc_start: 0.9117 (pm20) cc_final: 0.8887 (pm20) REVERT: A 1083 HIS cc_start: 0.8477 (t-90) cc_final: 0.8173 (t-90) REVERT: B 271 GLN cc_start: 0.8320 (mp10) cc_final: 0.8063 (mp10) REVERT: B 365 TYR cc_start: 0.8374 (m-10) cc_final: 0.8108 (m-10) REVERT: B 1072 GLU cc_start: 0.8994 (pm20) cc_final: 0.8464 (pm20) REVERT: B 1083 HIS cc_start: 0.8277 (t-90) cc_final: 0.8072 (t-90) REVERT: B 1139 ASP cc_start: 0.8806 (t0) cc_final: 0.8511 (t0) REVERT: E 1064 HIS cc_start: 0.8272 (m170) cc_final: 0.7899 (m170) REVERT: E 1072 GLU cc_start: 0.8995 (pm20) cc_final: 0.8592 (pm20) REVERT: E 1083 HIS cc_start: 0.8279 (t-90) cc_final: 0.7937 (t-90) REVERT: E 1139 ASP cc_start: 0.8850 (t0) cc_final: 0.8527 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1493 time to fit residues: 31.6634 Evaluate side-chains 91 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 219 optimal weight: 0.5980 chunk 415 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 395 optimal weight: 40.0000 chunk 296 optimal weight: 9.9990 chunk 372 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.093745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071395 restraints weight = 118917.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.068878 restraints weight = 105751.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069958 restraints weight = 115361.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.069709 restraints weight = 88565.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069880 restraints weight = 81117.088| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.089 26832 Z= 0.464 Angle : 0.823 9.469 37208 Z= 0.442 Chirality : 0.051 0.323 4624 Planarity : 0.006 0.084 5046 Dihedral : 6.170 50.239 5860 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.13), residues: 4242 helix: 0.76 (0.20), residues: 663 sheet: -0.07 (0.14), residues: 1248 loop : -0.52 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1091 TYR 0.030 0.003 TYR E1047 PHE 0.041 0.004 PHE E 906 TRP 0.057 0.004 TRP B 886 HIS 0.019 0.004 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00984 (26712) covalent geometry : angle 0.79909 (36899) SS BOND : bond 0.00703 ( 51) SS BOND : angle 1.96150 ( 102) hydrogen bonds : bond 0.05853 ( 1400) hydrogen bonds : angle 6.55172 ( 3759) link_BETA1-4 : bond 0.00272 ( 18) link_BETA1-4 : angle 1.49443 ( 54) link_NAG-ASN : bond 0.00911 ( 51) link_NAG-ASN : angle 2.74719 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.887 Fit side-chains REVERT: A 365 TYR cc_start: 0.8538 (m-10) cc_final: 0.8275 (m-10) REVERT: A 1072 GLU cc_start: 0.9148 (pm20) cc_final: 0.8554 (pm20) REVERT: A 1083 HIS cc_start: 0.8680 (t-90) cc_final: 0.8252 (t70) REVERT: A 1139 ASP cc_start: 0.8773 (t70) cc_final: 0.8481 (t0) REVERT: B 271 GLN cc_start: 0.8557 (mp10) cc_final: 0.8320 (mp10) REVERT: B 365 TYR cc_start: 0.8476 (m-10) cc_final: 0.8137 (m-10) REVERT: B 1072 GLU cc_start: 0.9073 (pm20) cc_final: 0.8451 (pm20) REVERT: B 1139 ASP cc_start: 0.8857 (t0) cc_final: 0.8544 (t0) REVERT: E 365 TYR cc_start: 0.8546 (m-10) cc_final: 0.8265 (m-10) REVERT: E 781 VAL cc_start: 0.9443 (t) cc_final: 0.9201 (p) REVERT: E 900 MET cc_start: 0.8066 (mmt) cc_final: 0.7800 (mmt) REVERT: E 1064 HIS cc_start: 0.8501 (m170) cc_final: 0.8111 (m170) REVERT: E 1072 GLU cc_start: 0.8998 (pm20) cc_final: 0.8398 (pm20) REVERT: E 1083 HIS cc_start: 0.8579 (t-90) cc_final: 0.8127 (t-90) REVERT: E 1139 ASP cc_start: 0.8912 (t0) cc_final: 0.8557 (t0) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1287 time to fit residues: 24.0523 Evaluate side-chains 83 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 425 optimal weight: 7.9990 chunk 301 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 362 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 249 optimal weight: 30.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.097357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075708 restraints weight = 116540.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074246 restraints weight = 110073.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074848 restraints weight = 100130.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.075157 restraints weight = 76418.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075264 restraints weight = 71111.096| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26832 Z= 0.144 Angle : 0.562 9.774 37208 Z= 0.292 Chirality : 0.046 0.264 4624 Planarity : 0.005 0.051 5046 Dihedral : 5.288 39.614 5860 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.13), residues: 4242 helix: 1.54 (0.20), residues: 672 sheet: 0.05 (0.14), residues: 1269 loop : -0.36 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 905 TYR 0.014 0.001 TYR B 904 PHE 0.027 0.002 PHE E 906 TRP 0.020 0.001 TRP B 886 HIS 0.007 0.001 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00305 (26712) covalent geometry : angle 0.53410 (36899) SS BOND : bond 0.00386 ( 51) SS BOND : angle 1.65853 ( 102) hydrogen bonds : bond 0.03553 ( 1400) hydrogen bonds : angle 5.64187 ( 3759) link_BETA1-4 : bond 0.00393 ( 18) link_BETA1-4 : angle 1.04796 ( 54) link_NAG-ASN : bond 0.00443 ( 51) link_NAG-ASN : angle 2.42202 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.881 Fit side-chains REVERT: A 365 TYR cc_start: 0.8309 (m-10) cc_final: 0.8041 (m-10) REVERT: A 900 MET cc_start: 0.7638 (mmt) cc_final: 0.7391 (mmp) REVERT: A 1072 GLU cc_start: 0.9047 (pm20) cc_final: 0.8809 (pm20) REVERT: A 1083 HIS cc_start: 0.8492 (t-90) cc_final: 0.8208 (t-90) REVERT: A 1139 ASP cc_start: 0.8746 (t70) cc_final: 0.8540 (t0) REVERT: B 271 GLN cc_start: 0.8495 (mp10) cc_final: 0.8183 (mp10) REVERT: B 365 TYR cc_start: 0.8246 (m-10) cc_final: 0.7967 (m-10) REVERT: B 1072 GLU cc_start: 0.8953 (pm20) cc_final: 0.8400 (pm20) REVERT: B 1083 HIS cc_start: 0.8291 (t-90) cc_final: 0.8076 (t-90) REVERT: B 1139 ASP cc_start: 0.8853 (t0) cc_final: 0.8532 (t0) REVERT: E 365 TYR cc_start: 0.8264 (m-10) cc_final: 0.8049 (m-10) REVERT: E 900 MET cc_start: 0.8180 (mmt) cc_final: 0.7320 (mmm) REVERT: E 1064 HIS cc_start: 0.8177 (m170) cc_final: 0.7934 (m170) REVERT: E 1072 GLU cc_start: 0.8936 (pm20) cc_final: 0.8471 (pm20) REVERT: E 1083 HIS cc_start: 0.8268 (t-90) cc_final: 0.7947 (t-90) REVERT: E 1139 ASP cc_start: 0.8818 (t0) cc_final: 0.8512 (t0) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1277 time to fit residues: 25.4890 Evaluate side-chains 89 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 261 optimal weight: 50.0000 chunk 189 optimal weight: 30.0000 chunk 396 optimal weight: 50.0000 chunk 131 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 383 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 366 optimal weight: 10.0000 chunk 425 optimal weight: 4.9990 chunk 356 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.091933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070158 restraints weight = 119519.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068037 restraints weight = 115760.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068608 restraints weight = 124754.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.068999 restraints weight = 87368.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069146 restraints weight = 80039.254| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.098 26832 Z= 0.571 Angle : 0.923 11.294 37208 Z= 0.496 Chirality : 0.053 0.275 4624 Planarity : 0.007 0.085 5046 Dihedral : 6.691 47.834 5860 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.20 % Favored : 91.77 % Rotamer: Outliers : 0.09 % Allowed : 0.87 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.13), residues: 4242 helix: 0.34 (0.19), residues: 648 sheet: -0.54 (0.14), residues: 1269 loop : -0.92 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1000 TYR 0.033 0.004 TYR E1047 PHE 0.050 0.004 PHE B 275 TRP 0.079 0.006 TRP B 886 HIS 0.017 0.005 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.01215 (26712) covalent geometry : angle 0.89783 (36899) SS BOND : bond 0.00759 ( 51) SS BOND : angle 2.11142 ( 102) hydrogen bonds : bond 0.06482 ( 1400) hydrogen bonds : angle 6.95267 ( 3759) link_BETA1-4 : bond 0.00343 ( 18) link_BETA1-4 : angle 1.67500 ( 54) link_NAG-ASN : bond 0.01028 ( 51) link_NAG-ASN : angle 2.97606 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.874 Fit side-chains REVERT: A 900 MET cc_start: 0.7948 (mmt) cc_final: 0.7684 (mmt) REVERT: A 1072 GLU cc_start: 0.9144 (pm20) cc_final: 0.8567 (pm20) REVERT: A 1083 HIS cc_start: 0.8681 (t-90) cc_final: 0.8226 (t70) REVERT: A 1139 ASP cc_start: 0.8764 (t70) cc_final: 0.8490 (t0) REVERT: B 365 TYR cc_start: 0.8331 (m-10) cc_final: 0.8068 (m-10) REVERT: B 781 VAL cc_start: 0.9438 (p) cc_final: 0.9030 (p) REVERT: B 1017 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7808 (tm-30) REVERT: B 1072 GLU cc_start: 0.9102 (pm20) cc_final: 0.8544 (pm20) REVERT: B 1083 HIS cc_start: 0.8613 (t-90) cc_final: 0.8172 (t70) REVERT: B 1139 ASP cc_start: 0.8731 (t0) cc_final: 0.8411 (t0) REVERT: E 365 TYR cc_start: 0.8480 (m-10) cc_final: 0.8221 (m-10) REVERT: E 900 MET cc_start: 0.8255 (mmt) cc_final: 0.7791 (mmt) REVERT: E 1064 HIS cc_start: 0.8552 (m170) cc_final: 0.8219 (m170) REVERT: E 1072 GLU cc_start: 0.9029 (pm20) cc_final: 0.8406 (pm20) REVERT: E 1139 ASP cc_start: 0.8823 (t0) cc_final: 0.8505 (t0) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1191 time to fit residues: 20.4384 Evaluate side-chains 85 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 107 optimal weight: 20.0000 chunk 133 optimal weight: 50.0000 chunk 185 optimal weight: 9.9990 chunk 112 optimal weight: 40.0000 chunk 180 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 421 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 119 optimal weight: 50.0000 chunk 87 optimal weight: 0.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 ASN E1054 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.090372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068824 restraints weight = 119018.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066463 restraints weight = 113328.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067263 restraints weight = 131364.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067186 restraints weight = 98199.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.067884 restraints weight = 84827.875| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.119 26832 Z= 0.655 Angle : 1.055 12.636 37208 Z= 0.567 Chirality : 0.056 0.300 4624 Planarity : 0.008 0.071 5046 Dihedral : 8.106 54.668 5860 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.62 % Favored : 90.33 % Rotamer: Outliers : 0.09 % Allowed : 0.96 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.12), residues: 4242 helix: -0.93 (0.18), residues: 690 sheet: -1.03 (0.15), residues: 1131 loop : -1.59 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1000 TYR 0.040 0.004 TYR E 904 PHE 0.087 0.006 PHE A 275 TRP 0.091 0.007 TRP B 886 HIS 0.018 0.005 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.01396 (26712) covalent geometry : angle 1.02536 (36899) SS BOND : bond 0.00809 ( 51) SS BOND : angle 2.24960 ( 102) hydrogen bonds : bond 0.07173 ( 1400) hydrogen bonds : angle 7.89476 ( 3759) link_BETA1-4 : bond 0.00407 ( 18) link_BETA1-4 : angle 1.72695 ( 54) link_NAG-ASN : bond 0.01329 ( 51) link_NAG-ASN : angle 3.53812 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.31 seconds wall clock time: 55 minutes 33.85 seconds (3333.85 seconds total)