Starting phenix.real_space_refine on Fri Feb 6 21:52:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8l_46641/02_2026/9d8l_46641.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8l_46641/02_2026/9d8l_46641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d8l_46641/02_2026/9d8l_46641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8l_46641/02_2026/9d8l_46641.map" model { file = "/net/cci-nas-00/data/ceres_data/9d8l_46641/02_2026/9d8l_46641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8l_46641/02_2026/9d8l_46641.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.018 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 119 5.16 5 C 17643 2.51 5 N 4492 2.21 5 O 5405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27659 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 9034 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1127, 8837 Classifications: {'peptide': 1127} Link IDs: {'PTRANS': 54, 'TRANS': 1072} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1127, 8837 Classifications: {'peptide': 1127} Link IDs: {'PTRANS': 54, 'TRANS': 1072} Chain breaks: 2 bond proxies already assigned to first conformer: 8850 Chain: "B" Number of atoms: 8875 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1106, 8678 Classifications: {'peptide': 1106} Link IDs: {'PTRANS': 54, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1106, 8678 Classifications: {'peptide': 1106} Link IDs: {'PTRANS': 54, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8689 Chain: "C" Number of atoms: 8866 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1105, 8669 Classifications: {'peptide': 1105} Link IDs: {'PTRANS': 54, 'TRANS': 1050} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1105, 8669 Classifications: {'peptide': 1105} Link IDs: {'PTRANS': 54, 'TRANS': 1050} Chain breaks: 2 bond proxies already assigned to first conformer: 8680 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 69 residue: pdb=" N AASP A1135 " occ=0.54 ... (14 atoms not shown) pdb=" OD2BASP A1135 " occ=0.46 residue: pdb=" N APRO A1136 " occ=0.54 ... (12 atoms not shown) pdb=" CD BPRO A1136 " occ=0.46 residue: pdb=" N ALEU A1137 " occ=0.54 ... (14 atoms not shown) pdb=" CD2BLEU A1137 " occ=0.46 residue: pdb=" N AGLN A1138 " occ=0.54 ... (16 atoms not shown) pdb=" NE2BGLN A1138 " occ=0.46 residue: pdb=" N ALEU A1139 " occ=0.54 ... (14 atoms not shown) pdb=" CD2BLEU A1139 " occ=0.46 residue: pdb=" N AGLU A1140 " occ=0.54 ... (16 atoms not shown) pdb=" OE2BGLU A1140 " occ=0.46 residue: pdb=" N ALEU A1141 " occ=0.54 ... (14 atoms not shown) pdb=" CD2BLEU A1141 " occ=0.46 residue: pdb=" N AASP A1142 " occ=0.54 ... (14 atoms not shown) pdb=" OD2BASP A1142 " occ=0.46 residue: pdb=" N ASER A1143 " occ=0.54 ... (10 atoms not shown) pdb=" OG BSER A1143 " occ=0.46 residue: pdb=" N APHE A1144 " occ=0.54 ... (20 atoms not shown) pdb=" CZ BPHE A1144 " occ=0.46 residue: pdb=" N ALYS A1145 " occ=0.54 ... (16 atoms not shown) pdb=" NZ BLYS A1145 " occ=0.46 residue: pdb=" N AGLU A1146 " occ=0.54 ... (16 atoms not shown) pdb=" OE2BGLU A1146 " occ=0.46 ... (remaining 57 not shown) Time building chain proxies: 10.46, per 1000 atoms: 0.38 Number of scatterers: 27659 At special positions: 0 Unit cell: (143.668, 159.061, 213.303, 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 119 16.00 O 5405 8.00 N 4492 7.00 C 17643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 3 " " NAG T 1 " - " FUC T 3 " NAG-ASN " NAG A1401 " - " ASN A1070 " " NAG A1402 " - " ASN A1094 " " NAG A1403 " - " ASN A 612 " " NAG A1404 " - " ASN A 231 " " NAG A1405 " - " ASN A 62 " " NAG A1406 " - " ASN A 121 " " NAG A1407 " - " ASN A 163 " " NAG A1408 " - " ASN A 351 " " NAG B1401 " - " ASN B1070 " " NAG B1402 " - " ASN B1094 " " NAG B1403 " - " ASN B 612 " " NAG B1404 " - " ASN B 231 " " NAG B1405 " - " ASN B 121 " " NAG B1406 " - " ASN B 163 " " NAG B1407 " - " ASN B 62 " " NAG B1408 " - " ASN B 351 " " NAG C1401 " - " ASN C 328 " " NAG C1402 " - " ASN C1070 " " NAG C1403 " - " ASN C1094 " " NAG C1404 " - " ASN C 62 " " NAG C1405 " - " ASN C 121 " " NAG C1406 " - " ASN C 163 " " NAG C1407 " - " ASN C 612 " " NAG C1408 " - " ASN C 340 " " NAG C1409 " - " ASN C 231 " " NAG D 1 " - " ASN A 279 " " NAG E 1 " - " ASN A 705 " " NAG F 1 " - " ASN A 713 " " NAG G 1 " - " ASN A 797 " " NAG H 1 " - " ASN A1130 " " NAG I 1 " - " ASN A 328 " " NAG J 1 " - " ASN B 797 " " NAG K 1 " - " ASN B1130 " " NAG L 1 " - " ASN B 328 " " NAG M 1 " - " ASN B 279 " " NAG N 1 " - " ASN B 705 " " NAG O 1 " - " ASN B 713 " " NAG P 1 " - " ASN C 279 " " NAG Q 1 " - " ASN C 705 " " NAG R 1 " - " ASN C 713 " " NAG S 1 " - " ASN C 797 " " NAG T 1 " - " ASN C1130 " " NAG U 1 " - " ASN C 351 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 2.3 seconds 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6384 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 51 sheets defined 25.6% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.760A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.112A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.539A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.526A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 756 through 779 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 887 removed outlier: 3.982A pdb=" N GLY A 887 " --> pdb=" O PHE A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 908 through 914 removed outlier: 4.089A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 929 Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 942 through 961 Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.606A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1157 removed outlier: 3.530A pdb=" N AGLU A1147 " --> pdb=" O ASER A1143 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N BHIS A1155 " --> pdb=" O BTYR A1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 Processing helix chain 'B' and resid 362 through 368 Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.657A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.596A pdb=" N SER B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 742 through 750 Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 756 through 779 removed outlier: 3.773A pdb=" N PHE B 778 " --> pdb=" O THR B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 893 through 904 Processing helix chain 'B' and resid 908 through 914 removed outlier: 4.143A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 929 Processing helix chain 'B' and resid 941 through 961 removed outlier: 3.973A pdb=" N GLN B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.379A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1157 removed outlier: 3.782A pdb=" N BHIS B1155 " --> pdb=" O BTYR B1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.978A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.630A pdb=" N ASN C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 368' Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.523A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 407 removed outlier: 3.955A pdb=" N VAL C 404 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER C 405 " --> pdb=" O ASN C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 removed outlier: 3.515A pdb=" N ASN C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 612 through 622 Processing helix chain 'C' and resid 733 through 738 Processing helix chain 'C' and resid 742 through 750 Processing helix chain 'C' and resid 751 through 753 No H-bonds generated for 'chain 'C' and resid 751 through 753' Processing helix chain 'C' and resid 754 through 779 removed outlier: 3.551A pdb=" N ASP C 771 " --> pdb=" O ALA C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 881 through 887 removed outlier: 4.040A pdb=" N PHE C 884 " --> pdb=" O GLY C 881 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY C 887 " --> pdb=" O PHE C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 904 Processing helix chain 'C' and resid 909 through 915 Processing helix chain 'C' and resid 915 through 929 Processing helix chain 'C' and resid 929 through 934 Processing helix chain 'C' and resid 941 through 961 removed outlier: 4.245A pdb=" N GLN C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 removed outlier: 3.561A pdb=" N ILE C 976 " --> pdb=" O VAL C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 1029 removed outlier: 5.492A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1157 removed outlier: 3.801A pdb=" N BHIS C1155 " --> pdb=" O BTYR C1151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.449A pdb=" N ASN A 62 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR A 266 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 264 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 261 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 189 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 204 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 193 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 200 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE A 199 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP A 225 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE A 201 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 56 removed outlier: 3.766A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 4.346A pdb=" N GLY A 102 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA A 240 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 100 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG A 101 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP A 103 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 153 removed outlier: 4.073A pdb=" N LEU A 140 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 241 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 243 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS A 144 " --> pdb=" O ARG A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.950A pdb=" N VAL A 591 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN A 314 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY A 589 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 325 removed outlier: 5.393A pdb=" N ASP A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 571 " --> pdb=" O GLY A 562 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE A 561 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 7.829A pdb=" N ASN A 434 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE A 371 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.895A pdb=" N CYS A 358 " --> pdb=" O CYS A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB2, first strand: chain 'A' and resid 650 through 656 removed outlier: 5.132A pdb=" N THR A 692 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN A 654 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.826A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 724 removed outlier: 6.041A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.547A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 784 through 786 removed outlier: 5.289A pdb=" N ILE A 784 " --> pdb=" O ASN C 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1116 through 1121 removed outlier: 4.988A pdb=" N ALA A1083 " --> pdb=" O SER A1119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.712A pdb=" N THR B 30 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 64 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 187 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 206 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 189 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N PHE B 199 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP B 225 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE B 201 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 56 removed outlier: 4.013A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.959A pdb=" N GLU B 131 " --> pdb=" O CYS B 164 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS B 164 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 149 through 153 removed outlier: 3.720A pdb=" N VAL B 142 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG B 243 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS B 144 " --> pdb=" O ARG B 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.341A pdb=" N ILE B 309 " --> pdb=" O THR B 595 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR B 595 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLN B 311 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 593 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.647A pdb=" N ALA B 373 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ASN B 434 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE B 371 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 358 through 359 removed outlier: 7.008A pdb=" N CYS B 358 " --> pdb=" O CYS B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC7, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC8, first strand: chain 'B' and resid 535 through 539 removed outlier: 5.210A pdb=" N ASP B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE B 561 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 656 removed outlier: 5.043A pdb=" N THR B 692 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASN B 654 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 687 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 668 " --> pdb=" O PRO B 661 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 698 through 700 removed outlier: 5.196A pdb=" N ILE C 784 " --> pdb=" O ASN B 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 707 through 711 removed outlier: 3.807A pdb=" N ILE B 710 " --> pdb=" O LYS B1069 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE B1091 " --> pdb=" O ALA B1074 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 714 through 718 removed outlier: 7.069A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 721 through 724 Processing sheet with id=AD5, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.490A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1116 through 1121 removed outlier: 5.691A pdb=" N VAL B1118 " --> pdb=" O PHE B1085 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE B1085 " --> pdb=" O VAL B1118 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY B1120 " --> pdb=" O ALA B1083 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.514A pdb=" N SER C 28 " --> pdb=" O TRP C 65 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 187 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 193 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 224 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER C 203 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 49 through 56 removed outlier: 3.832A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.963A pdb=" N ILE C 69 " --> pdb=" O ARG C 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.645A pdb=" N LEU C 83 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY C 102 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG C 101 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 170 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 166 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 149 through 153 removed outlier: 3.608A pdb=" N SER C 149 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C 151 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.880A pdb=" N VAL C 591 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN C 314 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY C 589 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.511A pdb=" N VAL C 430 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AE6, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE7, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.630A pdb=" N TYR C 485 " --> pdb=" O TYR C 470 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AE9, first strand: chain 'C' and resid 547 through 550 removed outlier: 3.997A pdb=" N THR C 549 " --> pdb=" O ASP C 582 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA C 571 " --> pdb=" O GLY C 562 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 650 through 651 removed outlier: 5.942A pdb=" N GLU C 650 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR C 692 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 666 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 707 through 711 removed outlier: 3.616A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 714 through 724 removed outlier: 6.904A pdb=" N VAL C1061 " --> pdb=" O LEU C1045 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 714 through 724 removed outlier: 3.501A pdb=" N ALA C1052 " --> pdb=" O GLY C1055 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 729 through 731 removed outlier: 4.532A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1116 through 1121 removed outlier: 4.278A pdb=" N ALA C1083 " --> pdb=" O SER C1119 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3114 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: 6.09 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8628 1.34 - 1.46: 5775 1.46 - 1.58: 13760 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 28315 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" C2 NAG K 1 " ideal model delta sigma weight residual 1.532 1.561 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C THR B 626 " pdb=" N PRO B 627 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.01e-02 9.80e+03 1.83e+00 bond pdb=" C4 NAG E 1 " pdb=" C5 NAG E 1 " ideal model delta sigma weight residual 1.532 1.558 -0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" CB CYS A 734 " pdb=" SG CYS A 734 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.51e+00 bond pdb=" C1 NAG A1405 " pdb=" C2 NAG A1405 " ideal model delta sigma weight residual 1.532 1.556 -0.024 2.00e-02 2.50e+03 1.42e+00 ... (remaining 28310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 37953 2.02 - 4.03: 474 4.03 - 6.05: 71 6.05 - 8.06: 8 8.06 - 10.08: 7 Bond angle restraints: 38513 Sorted by residual: angle pdb=" N VAL A 566 " pdb=" CA VAL A 566 " pdb=" C VAL A 566 " ideal model delta sigma weight residual 111.91 107.41 4.50 8.90e-01 1.26e+00 2.55e+01 angle pdb=" N HIS A 515 " pdb=" CA HIS A 515 " pdb=" C HIS A 515 " ideal model delta sigma weight residual 114.56 108.68 5.88 1.27e+00 6.20e-01 2.14e+01 angle pdb=" C HIS C 515 " pdb=" N ALA C 516 " pdb=" CA ALA C 516 " ideal model delta sigma weight residual 121.80 131.36 -9.56 2.44e+00 1.68e-01 1.53e+01 angle pdb=" N ASN B 62 " pdb=" CA ASN B 62 " pdb=" CB ASN B 62 " ideal model delta sigma weight residual 110.29 116.00 -5.71 1.52e+00 4.33e-01 1.41e+01 angle pdb=" C1 NAG B1407 " pdb=" C2 NAG B1407 " pdb=" C3 NAG B1407 " ideal model delta sigma weight residual 109.80 99.72 10.08 3.00e+00 1.11e-01 1.13e+01 ... (remaining 38508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15293 17.91 - 35.81: 1708 35.81 - 53.72: 511 53.72 - 71.62: 103 71.62 - 89.53: 46 Dihedral angle restraints: 17661 sinusoidal: 7725 harmonic: 9936 Sorted by residual: dihedral pdb=" CB CYS A1078 " pdb=" SG CYS A1078 " pdb=" SG CYS A1122 " pdb=" CB CYS A1122 " ideal model delta sinusoidal sigma weight residual -86.00 -7.04 -78.96 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS C 658 " pdb=" SG CYS C 658 " pdb=" SG CYS C 667 " pdb=" CB CYS C 667 " ideal model delta sinusoidal sigma weight residual -86.00 -12.55 -73.45 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS B1078 " pdb=" SG CYS B1078 " pdb=" SG CYS B1122 " pdb=" CB CYS B1122 " ideal model delta sinusoidal sigma weight residual -86.00 -14.96 -71.04 1 1.00e+01 1.00e-02 6.48e+01 ... (remaining 17658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 4494 0.206 - 0.412: 10 0.412 - 0.619: 3 0.619 - 0.825: 0 0.825 - 1.031: 1 Chirality restraints: 4508 Sorted by residual: chirality pdb=" C1 NAG B1407 " pdb=" ND2 ASN B 62 " pdb=" C2 NAG B1407 " pdb=" O5 NAG B1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 797 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.14e+00 chirality pdb=" C1 NAG C1409 " pdb=" ND2 ASN C 231 " pdb=" C2 NAG C1409 " pdb=" O5 NAG C1409 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.99e+00 ... (remaining 4505 not shown) Planarity restraints: 4927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 62 " 0.040 2.00e-02 2.50e+03 3.74e-02 1.75e+01 pdb=" CG ASN B 62 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 62 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 62 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG B1407 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 797 " 0.029 2.00e-02 2.50e+03 2.69e-02 9.07e+00 pdb=" CG ASN C 797 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN C 797 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 797 " -0.029 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 62 " 0.004 2.00e-02 2.50e+03 2.48e-02 7.68e+00 pdb=" CG ASN A 62 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 62 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 62 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG A1405 " 0.022 2.00e-02 2.50e+03 ... (remaining 4924 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 603 2.68 - 3.23: 25960 3.23 - 3.79: 43054 3.79 - 4.34: 56039 4.34 - 4.90: 94849 Nonbonded interactions: 220505 Sorted by model distance: nonbonded pdb=" OG1 THR C 390 " pdb=" OE1 GLU C 512 " model vdw 2.121 3.040 nonbonded pdb=" N GLU C 744 " pdb=" OE1 GLU C 744 " model vdw 2.160 3.120 nonbonded pdb=" OD1 ASN B 62 " pdb=" N2 NAG B1407 " model vdw 2.171 3.120 nonbonded pdb=" OH TYR A 752 " pdb=" OD1 ASP A 990 " model vdw 2.180 3.040 nonbonded pdb=" O PRO C 84 " pdb=" OH TYR C 266 " model vdw 2.194 3.040 ... (remaining 220500 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 823 or resid 850 through 1134 or resid 1401 thr \ ough 1408)) selection = (chain 'B' and (resid 15 through 823 or resid 850 through 1134 or resid 1401 thr \ ough 1408)) selection = (chain 'C' and (resid 15 through 1134 or resid 1401 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 31.310 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28422 Z= 0.147 Angle : 0.610 17.768 38791 Z= 0.290 Chirality : 0.050 1.031 4508 Planarity : 0.003 0.049 4884 Dihedral : 16.659 89.531 11148 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.49 % Favored : 95.39 % Rotamer: Outliers : 3.51 % Allowed : 24.01 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.13 (0.15), residues: 3389 helix: 2.35 (0.18), residues: 799 sheet: -0.03 (0.20), residues: 731 loop : -0.90 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 761 TYR 0.029 0.001 TYR B 900 PHE 0.020 0.001 PHE A 819 TRP 0.017 0.001 TRP C 65 HIS 0.004 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00339 (28315) covalent geometry : angle 0.55809 (38513) SS BOND : bond 0.00201 ( 43) SS BOND : angle 1.06530 ( 86) hydrogen bonds : bond 0.19664 ( 1126) hydrogen bonds : angle 7.78856 ( 3114) link_BETA1-4 : bond 0.00500 ( 18) link_BETA1-4 : angle 2.00813 ( 54) link_BETA1-6 : bond 0.00307 ( 3) link_BETA1-6 : angle 1.34333 ( 9) link_NAG-ASN : bond 0.00736 ( 43) link_NAG-ASN : angle 4.03699 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.5440 (ttt180) cc_final: 0.4380 (tmm-80) REVERT: A 188 ARG cc_start: 0.7358 (ttp-170) cc_final: 0.7117 (ttp-170) REVERT: A 268 GLN cc_start: 0.8885 (mt0) cc_final: 0.8439 (tt0) REVERT: A 326 PHE cc_start: 0.8371 (m-80) cc_final: 0.7941 (m-10) REVERT: A 328 ASN cc_start: 0.6932 (OUTLIER) cc_final: 0.6554 (m-40) REVERT: A 574 ASP cc_start: 0.8339 (t0) cc_final: 0.7734 (t70) REVERT: A 579 GLU cc_start: 0.7688 (tt0) cc_final: 0.7366 (mt-10) REVERT: A 736 MET cc_start: 0.8916 (tpp) cc_final: 0.8340 (tpp) REVERT: A 1080 ASP cc_start: 0.8747 (m-30) cc_final: 0.7954 (p0) REVERT: B 151 MET cc_start: -0.0283 (pp-130) cc_final: -0.1862 (mtp) REVERT: B 168 TYR cc_start: 0.6798 (t80) cc_final: 0.6519 (t80) REVERT: B 236 GLN cc_start: 0.8222 (tt0) cc_final: 0.7904 (tt0) REVERT: B 542 LEU cc_start: 0.7691 (tt) cc_final: 0.7294 (pp) REVERT: B 550 LYS cc_start: 0.7073 (ttmm) cc_final: 0.6678 (ptmm) REVERT: B 554 LYS cc_start: 0.8359 (tmtt) cc_final: 0.8001 (ttmt) REVERT: B 991 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7286 (ttm170) REVERT: C 17 MET cc_start: 0.3592 (mpp) cc_final: 0.2626 (pmm) REVERT: C 151 MET cc_start: 0.2577 (pp-130) cc_final: 0.1069 (pmm) REVERT: C 198 TYR cc_start: 0.7933 (m-80) cc_final: 0.7685 (m-80) REVERT: C 336 HIS cc_start: 0.7259 (p-80) cc_final: 0.6896 (m-70) REVERT: C 450 TYR cc_start: 0.5492 (p90) cc_final: 0.4479 (p90) REVERT: C 464 ASP cc_start: 0.7461 (t0) cc_final: 0.7247 (t70) REVERT: C 525 LYS cc_start: 0.8538 (ptmt) cc_final: 0.7946 (mmtm) REVERT: C 632 TYR cc_start: 0.7668 (t80) cc_final: 0.7457 (t80) REVERT: C 686 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7604 (mp10) REVERT: C 812 SER cc_start: 0.8966 (p) cc_final: 0.8633 (t) REVERT: C 975 ASP cc_start: 0.7884 (t70) cc_final: 0.6655 (m-30) outliers start: 67 outliers final: 47 residues processed: 302 average time/residue: 0.1700 time to fit residues: 82.6465 Evaluate side-chains 228 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1101 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 969 ILE Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 1000 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.0570 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 540 ASN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 671 GLN B 897 GLN B 951 ASN C 162 ASN C 770 GLN C1155 HIS B Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.184044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.127085 restraints weight = 86081.977| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 4.18 r_work: 0.3286 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28422 Z= 0.198 Angle : 0.667 17.614 38791 Z= 0.326 Chirality : 0.048 0.505 4508 Planarity : 0.004 0.052 4884 Dihedral : 7.134 61.317 5066 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 3.91 % Allowed : 23.64 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.05 (0.15), residues: 3389 helix: 2.16 (0.18), residues: 799 sheet: -0.03 (0.19), residues: 767 loop : -0.93 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 843 TYR 0.025 0.002 TYR C1063 PHE 0.028 0.001 PHE A 33 TRP 0.015 0.002 TRP B 629 HIS 0.004 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00465 (28315) covalent geometry : angle 0.62118 (38513) SS BOND : bond 0.00376 ( 43) SS BOND : angle 1.54116 ( 86) hydrogen bonds : bond 0.04727 ( 1126) hydrogen bonds : angle 5.85632 ( 3114) link_BETA1-4 : bond 0.00397 ( 18) link_BETA1-4 : angle 1.93770 ( 54) link_BETA1-6 : bond 0.00215 ( 3) link_BETA1-6 : angle 1.51294 ( 9) link_NAG-ASN : bond 0.00589 ( 43) link_NAG-ASN : angle 3.88503 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 193 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7557 (t70) cc_final: 0.7330 (t70) REVERT: A 65 TRP cc_start: 0.7428 (t60) cc_final: 0.7181 (t60) REVERT: A 151 MET cc_start: 0.1356 (OUTLIER) cc_final: -0.0248 (pp-130) REVERT: A 188 ARG cc_start: 0.7617 (ttp-170) cc_final: 0.7400 (ttp-170) REVERT: A 268 GLN cc_start: 0.8636 (mt0) cc_final: 0.8300 (tt0) REVERT: A 326 PHE cc_start: 0.8264 (m-80) cc_final: 0.7937 (m-10) REVERT: A 736 MET cc_start: 0.8790 (tpp) cc_final: 0.8358 (tpp) REVERT: B 151 MET cc_start: -0.0353 (OUTLIER) cc_final: -0.1996 (mtp) REVERT: B 168 TYR cc_start: 0.7256 (t80) cc_final: 0.7054 (t80) REVERT: B 233 THR cc_start: 0.7778 (m) cc_final: 0.7547 (p) REVERT: B 236 GLN cc_start: 0.8584 (tt0) cc_final: 0.8268 (tt0) REVERT: B 361 ASP cc_start: 0.6692 (p0) cc_final: 0.6167 (t0) REVERT: B 528 ASN cc_start: 0.8222 (m-40) cc_final: 0.7648 (t0) REVERT: B 542 LEU cc_start: 0.7835 (tt) cc_final: 0.7491 (pp) REVERT: B 550 LYS cc_start: 0.7055 (ttmm) cc_final: 0.6753 (ptmm) REVERT: B 554 LYS cc_start: 0.8349 (tmtt) cc_final: 0.8021 (ttmt) REVERT: B 953 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8210 (tp40) REVERT: C 17 MET cc_start: 0.3386 (mpp) cc_final: 0.2613 (pmm) REVERT: C 151 MET cc_start: 0.3522 (pp-130) cc_final: 0.2163 (pmm) REVERT: C 336 HIS cc_start: 0.7495 (p-80) cc_final: 0.7100 (p-80) REVERT: C 362 TYR cc_start: 0.7863 (m-80) cc_final: 0.7663 (m-80) REVERT: C 389 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: C 463 ARG cc_start: 0.6848 (ttp80) cc_final: 0.5926 (ttm-80) REVERT: C 464 ASP cc_start: 0.7498 (t0) cc_final: 0.7247 (t70) REVERT: C 561 PHE cc_start: 0.8119 (p90) cc_final: 0.7841 (p90) REVERT: C 611 VAL cc_start: 0.9455 (p) cc_final: 0.9179 (m) REVERT: C 632 TYR cc_start: 0.7637 (t80) cc_final: 0.7400 (t80) REVERT: C 812 SER cc_start: 0.9071 (p) cc_final: 0.8702 (t) REVERT: C 975 ASP cc_start: 0.7934 (t70) cc_final: 0.6783 (m-30) outliers start: 78 outliers final: 49 residues processed: 255 average time/residue: 0.1701 time to fit residues: 71.1569 Evaluate side-chains 218 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 937 THR Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1093 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 134 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 281 optimal weight: 0.6980 chunk 262 optimal weight: 9.9990 chunk 272 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 314 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN B 910 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.185672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.129450 restraints weight = 91733.112| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 4.14 r_work: 0.3321 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28422 Z= 0.126 Angle : 0.600 16.847 38791 Z= 0.291 Chirality : 0.045 0.416 4508 Planarity : 0.003 0.053 4884 Dihedral : 6.611 58.725 5027 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 3.91 % Allowed : 23.34 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.08 (0.15), residues: 3389 helix: 2.33 (0.18), residues: 789 sheet: -0.05 (0.19), residues: 775 loop : -0.94 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 843 TYR 0.021 0.001 TYR C1063 PHE 0.031 0.001 PHE A 33 TRP 0.013 0.001 TRP C 65 HIS 0.003 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00285 (28315) covalent geometry : angle 0.55617 (38513) SS BOND : bond 0.00281 ( 43) SS BOND : angle 1.40210 ( 86) hydrogen bonds : bond 0.04070 ( 1126) hydrogen bonds : angle 5.46219 ( 3114) link_BETA1-4 : bond 0.00476 ( 18) link_BETA1-4 : angle 1.79545 ( 54) link_BETA1-6 : bond 0.00199 ( 3) link_BETA1-6 : angle 1.44010 ( 9) link_NAG-ASN : bond 0.00531 ( 43) link_NAG-ASN : angle 3.63039 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 194 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7374 (t60) cc_final: 0.7145 (t60) REVERT: A 188 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7256 (ttp-170) REVERT: A 268 GLN cc_start: 0.8620 (mt0) cc_final: 0.8285 (tt0) REVERT: A 326 PHE cc_start: 0.8222 (m-80) cc_final: 0.7957 (m-10) REVERT: A 736 MET cc_start: 0.8782 (tpp) cc_final: 0.8438 (tpp) REVERT: A 981 ASP cc_start: 0.7481 (p0) cc_final: 0.7076 (p0) REVERT: B 133 GLN cc_start: 0.8116 (tp40) cc_final: 0.7868 (mm-40) REVERT: B 151 MET cc_start: -0.0402 (pp-130) cc_final: -0.1978 (mtp) REVERT: B 168 TYR cc_start: 0.7236 (t80) cc_final: 0.7006 (t80) REVERT: B 361 ASP cc_start: 0.6800 (p0) cc_final: 0.6193 (t0) REVERT: B 524 LYS cc_start: 0.3191 (OUTLIER) cc_final: 0.2315 (mtpt) REVERT: B 542 LEU cc_start: 0.7868 (tt) cc_final: 0.7517 (pp) REVERT: B 554 LYS cc_start: 0.8325 (tmtt) cc_final: 0.7988 (ttmt) REVERT: B 953 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8211 (tp40) REVERT: B 988 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7660 (mm-40) REVERT: C 17 MET cc_start: 0.3387 (mpp) cc_final: 0.2692 (pmm) REVERT: C 151 MET cc_start: 0.3373 (pp-130) cc_final: 0.2098 (pmm) REVERT: C 336 HIS cc_start: 0.7521 (p-80) cc_final: 0.7277 (p-80) REVERT: C 463 ARG cc_start: 0.6860 (ttp80) cc_final: 0.5864 (ttm-80) REVERT: C 464 ASP cc_start: 0.7449 (t0) cc_final: 0.7211 (t70) REVERT: C 529 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7855 (tt) REVERT: C 561 PHE cc_start: 0.8151 (p90) cc_final: 0.7908 (p90) REVERT: C 611 VAL cc_start: 0.9428 (p) cc_final: 0.9136 (m) REVERT: C 632 TYR cc_start: 0.7667 (t80) cc_final: 0.7406 (t80) REVERT: C 750 LEU cc_start: 0.8772 (mm) cc_final: 0.8530 (pp) REVERT: C 812 SER cc_start: 0.9054 (p) cc_final: 0.8664 (t) REVERT: C 852 ASN cc_start: 0.7992 (t0) cc_final: 0.7601 (t0) REVERT: C 975 ASP cc_start: 0.7774 (t70) cc_final: 0.6697 (m-30) REVERT: C 1000 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9010 (tt) outliers start: 77 outliers final: 38 residues processed: 255 average time/residue: 0.1802 time to fit residues: 75.2537 Evaluate side-chains 221 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 988 GLN Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 797 ASN Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1093 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 239 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 162 optimal weight: 30.0000 chunk 321 optimal weight: 1.9990 chunk 43 optimal weight: 50.0000 chunk 254 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 133 GLN A 186 ASN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 903 ASN C 770 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.182507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125683 restraints weight = 89445.606| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 4.09 r_work: 0.3273 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28422 Z= 0.204 Angle : 0.638 15.506 38791 Z= 0.311 Chirality : 0.046 0.477 4508 Planarity : 0.004 0.052 4884 Dihedral : 6.547 58.066 5014 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.58 % Rotamer: Outliers : 4.45 % Allowed : 23.27 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.05 (0.15), residues: 3389 helix: 2.11 (0.18), residues: 794 sheet: -0.13 (0.19), residues: 787 loop : -0.99 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 843 TYR 0.034 0.002 TYR B 900 PHE 0.019 0.001 PHE C 371 TRP 0.014 0.002 TRP B 629 HIS 0.004 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00486 (28315) covalent geometry : angle 0.59692 (38513) SS BOND : bond 0.00326 ( 43) SS BOND : angle 1.46597 ( 86) hydrogen bonds : bond 0.04211 ( 1126) hydrogen bonds : angle 5.30859 ( 3114) link_BETA1-4 : bond 0.00443 ( 18) link_BETA1-4 : angle 1.85309 ( 54) link_BETA1-6 : bond 0.00112 ( 3) link_BETA1-6 : angle 1.63466 ( 9) link_NAG-ASN : bond 0.00509 ( 43) link_NAG-ASN : angle 3.59957 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 180 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TRP cc_start: 0.7361 (t60) cc_final: 0.7076 (t60) REVERT: A 151 MET cc_start: 0.1185 (OUTLIER) cc_final: -0.0279 (pp-130) REVERT: A 188 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.7051 (ttt180) REVERT: A 235 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7262 (p90) REVERT: A 268 GLN cc_start: 0.8659 (mt0) cc_final: 0.8294 (tt0) REVERT: A 326 PHE cc_start: 0.8304 (m-80) cc_final: 0.8002 (m-10) REVERT: A 736 MET cc_start: 0.8827 (tpp) cc_final: 0.8556 (tpp) REVERT: B 133 GLN cc_start: 0.8076 (tp40) cc_final: 0.7804 (mm-40) REVERT: B 151 MET cc_start: -0.0344 (OUTLIER) cc_final: -0.1954 (mtp) REVERT: B 168 TYR cc_start: 0.7339 (t80) cc_final: 0.7099 (t80) REVERT: B 236 GLN cc_start: 0.8602 (mt0) cc_final: 0.7864 (mm-40) REVERT: B 361 ASP cc_start: 0.6929 (p0) cc_final: 0.6392 (t0) REVERT: B 542 LEU cc_start: 0.7881 (tt) cc_final: 0.7460 (pp) REVERT: B 554 LYS cc_start: 0.8345 (tmtt) cc_final: 0.8006 (ttmt) REVERT: B 953 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8234 (tp40) REVERT: B 1046 MET cc_start: 0.8829 (ppp) cc_final: 0.8543 (ptt) REVERT: C 17 MET cc_start: 0.3352 (mpp) cc_final: 0.2774 (pmm) REVERT: C 151 MET cc_start: 0.3498 (OUTLIER) cc_final: 0.2296 (pmm) REVERT: C 198 TYR cc_start: 0.7869 (m-80) cc_final: 0.7549 (m-80) REVERT: C 464 ASP cc_start: 0.7469 (t0) cc_final: 0.7243 (t70) REVERT: C 511 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8107 (p90) REVERT: C 529 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7905 (tp) REVERT: C 611 VAL cc_start: 0.9461 (p) cc_final: 0.9179 (m) REVERT: C 632 TYR cc_start: 0.7635 (t80) cc_final: 0.7353 (t80) REVERT: C 812 SER cc_start: 0.9081 (p) cc_final: 0.8662 (t) REVERT: C 975 ASP cc_start: 0.7817 (t70) cc_final: 0.6736 (m-30) REVERT: C 1000 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9026 (tt) outliers start: 94 outliers final: 60 residues processed: 259 average time/residue: 0.1571 time to fit residues: 67.8628 Evaluate side-chains 240 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 937 THR Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1093 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 291 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 236 optimal weight: 0.5980 chunk 165 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 268 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 GLN A1131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.185857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.130485 restraints weight = 98819.478| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 4.13 r_work: 0.3328 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28422 Z= 0.100 Angle : 0.569 15.226 38791 Z= 0.276 Chirality : 0.044 0.474 4508 Planarity : 0.003 0.054 4884 Dihedral : 6.214 56.792 5012 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 3.51 % Allowed : 23.91 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.17 (0.15), residues: 3389 helix: 2.37 (0.18), residues: 795 sheet: 0.05 (0.19), residues: 785 loop : -0.92 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 843 TYR 0.020 0.001 TYR C1063 PHE 0.017 0.001 PHE C 371 TRP 0.012 0.001 TRP C 65 HIS 0.003 0.000 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00215 (28315) covalent geometry : angle 0.53054 (38513) SS BOND : bond 0.00219 ( 43) SS BOND : angle 1.05741 ( 86) hydrogen bonds : bond 0.03529 ( 1126) hydrogen bonds : angle 5.05294 ( 3114) link_BETA1-4 : bond 0.00488 ( 18) link_BETA1-4 : angle 1.58714 ( 54) link_BETA1-6 : bond 0.00264 ( 3) link_BETA1-6 : angle 1.36550 ( 9) link_NAG-ASN : bond 0.00511 ( 43) link_NAG-ASN : angle 3.38693 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 201 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7117 (ttt180) REVERT: A 235 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7262 (p90) REVERT: A 268 GLN cc_start: 0.8599 (mt0) cc_final: 0.8252 (tt0) REVERT: A 326 PHE cc_start: 0.8359 (m-80) cc_final: 0.8027 (m-10) REVERT: A 736 MET cc_start: 0.8780 (tpp) cc_final: 0.8478 (tpp) REVERT: B 133 GLN cc_start: 0.8118 (tp40) cc_final: 0.7844 (mm-40) REVERT: B 151 MET cc_start: -0.0478 (OUTLIER) cc_final: -0.1979 (mtp) REVERT: B 168 TYR cc_start: 0.7313 (t80) cc_final: 0.7075 (t80) REVERT: B 236 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8064 (tp40) REVERT: B 361 ASP cc_start: 0.7023 (p0) cc_final: 0.6399 (t0) REVERT: B 542 LEU cc_start: 0.7830 (tt) cc_final: 0.7482 (pp) REVERT: B 554 LYS cc_start: 0.8334 (tmtt) cc_final: 0.7981 (ttmt) REVERT: B 953 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8230 (tp40) REVERT: B 979 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7741 (mtm110) REVERT: B 988 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7715 (mm-40) REVERT: B 1046 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8522 (ptt) REVERT: C 17 MET cc_start: 0.3279 (mpp) cc_final: 0.2800 (pmm) REVERT: C 151 MET cc_start: 0.3458 (pp-130) cc_final: 0.2294 (pmm) REVERT: C 198 TYR cc_start: 0.7834 (m-80) cc_final: 0.7458 (m-80) REVERT: C 434 ASN cc_start: 0.7899 (p0) cc_final: 0.6890 (t0) REVERT: C 464 ASP cc_start: 0.7516 (t0) cc_final: 0.7284 (t70) REVERT: C 611 VAL cc_start: 0.9428 (p) cc_final: 0.9123 (m) REVERT: C 632 TYR cc_start: 0.7673 (t80) cc_final: 0.7383 (t80) REVERT: C 812 SER cc_start: 0.9049 (p) cc_final: 0.8606 (t) REVERT: C 852 ASN cc_start: 0.7950 (t0) cc_final: 0.7637 (t0) REVERT: C 975 ASP cc_start: 0.7747 (t70) cc_final: 0.6643 (m-30) outliers start: 65 outliers final: 44 residues processed: 253 average time/residue: 0.1790 time to fit residues: 73.5034 Evaluate side-chains 233 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 988 GLN Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 658 CYS Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 1093 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 139 optimal weight: 7.9990 chunk 285 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 237 optimal weight: 0.0980 chunk 122 optimal weight: 20.0000 chunk 185 optimal weight: 0.8980 chunk 258 optimal weight: 0.0270 chunk 131 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 849 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 = 0.4357 r_free = 0.4357 target = 0.186016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.132966 restraints weight = 89908.742| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 4.51 r_work: 0.3324 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28422 Z= 0.102 Angle : 0.563 14.602 38791 Z= 0.272 Chirality : 0.044 0.441 4508 Planarity : 0.003 0.053 4884 Dihedral : 5.980 57.456 5007 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 3.71 % Allowed : 23.70 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.20 (0.15), residues: 3389 helix: 2.42 (0.18), residues: 795 sheet: 0.01 (0.19), residues: 791 loop : -0.88 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 843 TYR 0.020 0.001 TYR A1063 PHE 0.019 0.001 PHE C 371 TRP 0.011 0.001 TRP A 629 HIS 0.008 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00224 (28315) covalent geometry : angle 0.52641 (38513) SS BOND : bond 0.00228 ( 43) SS BOND : angle 1.05491 ( 86) hydrogen bonds : bond 0.03468 ( 1126) hydrogen bonds : angle 4.94481 ( 3114) link_BETA1-4 : bond 0.00466 ( 18) link_BETA1-4 : angle 1.64570 ( 54) link_BETA1-6 : bond 0.00377 ( 3) link_BETA1-6 : angle 1.39587 ( 9) link_NAG-ASN : bond 0.00498 ( 43) link_NAG-ASN : angle 3.26122 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 188 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.6362 (OUTLIER) cc_final: 0.5075 (p) REVERT: A 77 ARG cc_start: 0.5590 (ttt180) cc_final: 0.5231 (tmm-80) REVERT: A 151 MET cc_start: 0.1228 (OUTLIER) cc_final: -0.0269 (pp-130) REVERT: A 188 ARG cc_start: 0.7656 (ttp-170) cc_final: 0.7075 (ttt180) REVERT: A 232 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6584 (mt) REVERT: A 235 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7348 (p90) REVERT: A 268 GLN cc_start: 0.8583 (mt0) cc_final: 0.8262 (tt0) REVERT: A 326 PHE cc_start: 0.8304 (m-80) cc_final: 0.8022 (m-10) REVERT: A 736 MET cc_start: 0.8780 (tpp) cc_final: 0.8465 (tpp) REVERT: B 133 GLN cc_start: 0.8075 (tp40) cc_final: 0.7810 (mm-40) REVERT: B 151 MET cc_start: -0.0462 (OUTLIER) cc_final: -0.1960 (mtp) REVERT: B 168 TYR cc_start: 0.7292 (t80) cc_final: 0.7063 (t80) REVERT: B 236 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8109 (tp40) REVERT: B 314 ASN cc_start: 0.8233 (m-40) cc_final: 0.7977 (m-40) REVERT: B 361 ASP cc_start: 0.7129 (p0) cc_final: 0.6422 (t0) REVERT: B 542 LEU cc_start: 0.7859 (tt) cc_final: 0.7525 (pp) REVERT: B 554 LYS cc_start: 0.8297 (tmtt) cc_final: 0.7974 (ttmt) REVERT: B 953 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8267 (tp40) REVERT: B 979 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7772 (mtm110) REVERT: B 988 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7643 (mm-40) REVERT: B 1046 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8474 (ptt) REVERT: C 17 MET cc_start: 0.3252 (mpp) cc_final: 0.2833 (pmm) REVERT: C 151 MET cc_start: 0.3343 (pp-130) cc_final: 0.2194 (pmm) REVERT: C 198 TYR cc_start: 0.7847 (m-80) cc_final: 0.7505 (m-80) REVERT: C 434 ASN cc_start: 0.7949 (p0) cc_final: 0.7086 (t0) REVERT: C 464 ASP cc_start: 0.7514 (t0) cc_final: 0.7305 (t70) REVERT: C 511 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7853 (p90) REVERT: C 611 VAL cc_start: 0.9438 (p) cc_final: 0.9150 (m) REVERT: C 632 TYR cc_start: 0.7659 (t80) cc_final: 0.7389 (t80) REVERT: C 812 SER cc_start: 0.9030 (p) cc_final: 0.8625 (t) REVERT: C 820 ASN cc_start: 0.8546 (t0) cc_final: 0.8298 (t0) REVERT: C 852 ASN cc_start: 0.7987 (t0) cc_final: 0.7708 (t0) REVERT: C 975 ASP cc_start: 0.7741 (t70) cc_final: 0.6628 (m-30) outliers start: 71 outliers final: 49 residues processed: 243 average time/residue: 0.1677 time to fit residues: 67.1101 Evaluate side-chains 240 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 182 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 988 GLN Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 658 CYS Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 1093 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 163 optimal weight: 8.9990 chunk 230 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 219 optimal weight: 0.0050 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 40.0000 chunk 131 optimal weight: 6.9990 chunk 160 optimal weight: 30.0000 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 GLN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN A1155 HIS B B 910 ASN C 162 ASN C 336 HIS C 868 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.181372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.125151 restraints weight = 91061.551| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.88 r_work: 0.3254 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 28422 Z= 0.268 Angle : 0.686 14.025 38791 Z= 0.337 Chirality : 0.048 0.561 4508 Planarity : 0.004 0.059 4884 Dihedral : 6.416 58.959 5007 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 4.28 % Allowed : 23.47 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.17 (0.14), residues: 3389 helix: 1.90 (0.18), residues: 806 sheet: -0.16 (0.19), residues: 778 loop : -1.04 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1103 TYR 0.039 0.002 TYR C 900 PHE 0.022 0.002 PHE A 66 TRP 0.018 0.002 TRP B 629 HIS 0.010 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00637 (28315) covalent geometry : angle 0.64851 (38513) SS BOND : bond 0.00338 ( 43) SS BOND : angle 1.62985 ( 86) hydrogen bonds : bond 0.04515 ( 1126) hydrogen bonds : angle 5.24375 ( 3114) link_BETA1-4 : bond 0.00429 ( 18) link_BETA1-4 : angle 1.82379 ( 54) link_BETA1-6 : bond 0.00144 ( 3) link_BETA1-6 : angle 1.73133 ( 9) link_NAG-ASN : bond 0.00516 ( 43) link_NAG-ASN : angle 3.52056 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 180 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.6413 (OUTLIER) cc_final: 0.5983 (p) REVERT: A 151 MET cc_start: 0.1301 (OUTLIER) cc_final: -0.0211 (pp-130) REVERT: A 188 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7483 (ttp-170) REVERT: A 235 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7217 (p90) REVERT: A 268 GLN cc_start: 0.8660 (mt0) cc_final: 0.8282 (tt0) REVERT: A 278 GLU cc_start: 0.7660 (pp20) cc_final: 0.7128 (tp30) REVERT: A 736 MET cc_start: 0.8797 (tpp) cc_final: 0.8549 (tpp) REVERT: A 810 LYS cc_start: 0.8671 (mptp) cc_final: 0.8359 (mtpt) REVERT: B 65 TRP cc_start: 0.6774 (t60) cc_final: 0.6339 (t60) REVERT: B 151 MET cc_start: -0.0338 (OUTLIER) cc_final: -0.1919 (ttp) REVERT: B 168 TYR cc_start: 0.7331 (t80) cc_final: 0.7086 (t80) REVERT: B 236 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8133 (tp40) REVERT: B 361 ASP cc_start: 0.7037 (p0) cc_final: 0.6475 (t0) REVERT: B 528 ASN cc_start: 0.8212 (m-40) cc_final: 0.7702 (t0) REVERT: B 554 LYS cc_start: 0.8343 (tmtt) cc_final: 0.7982 (ttmt) REVERT: B 979 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7740 (mtm110) REVERT: C 17 MET cc_start: 0.3341 (mpp) cc_final: 0.2950 (pmm) REVERT: C 151 MET cc_start: 0.3624 (pp-130) cc_final: 0.2571 (pmm) REVERT: C 198 TYR cc_start: 0.7920 (m-80) cc_final: 0.7570 (m-80) REVERT: C 199 PHE cc_start: 0.8118 (t80) cc_final: 0.7808 (t80) REVERT: C 434 ASN cc_start: 0.8072 (p0) cc_final: 0.7253 (t0) REVERT: C 464 ASP cc_start: 0.7548 (t0) cc_final: 0.7314 (t70) REVERT: C 511 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8025 (p90) REVERT: C 529 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8011 (tp) REVERT: C 611 VAL cc_start: 0.9479 (p) cc_final: 0.9200 (m) REVERT: C 632 TYR cc_start: 0.7540 (t80) cc_final: 0.7263 (t80) REVERT: C 812 SER cc_start: 0.9084 (p) cc_final: 0.8652 (t) REVERT: C 852 ASN cc_start: 0.8191 (t0) cc_final: 0.7860 (t0) REVERT: C 975 ASP cc_start: 0.7804 (t70) cc_final: 0.6737 (m-30) outliers start: 89 outliers final: 62 residues processed: 256 average time/residue: 0.1736 time to fit residues: 72.2770 Evaluate side-chains 240 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 171 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 937 THR Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 816 ASP Chi-restraints excluded: chain C residue 969 ILE Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 219 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 152 optimal weight: 40.0000 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 45 optimal weight: 40.0000 chunk 156 optimal weight: 3.9990 chunk 316 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN B 205 HIS B 910 ASN B 953 GLN C 868 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.183379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.130085 restraints weight = 83979.600| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.37 r_work: 0.3286 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28422 Z= 0.133 Angle : 0.591 14.121 38791 Z= 0.288 Chirality : 0.045 0.480 4508 Planarity : 0.003 0.061 4884 Dihedral : 6.164 58.181 5006 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Rotamer: Outliers : 3.68 % Allowed : 23.84 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.01 (0.15), residues: 3389 helix: 2.09 (0.18), residues: 811 sheet: -0.16 (0.18), residues: 810 loop : -0.94 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1103 TYR 0.028 0.001 TYR C 900 PHE 0.029 0.001 PHE C 561 TRP 0.013 0.001 TRP A 629 HIS 0.012 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00308 (28315) covalent geometry : angle 0.55409 (38513) SS BOND : bond 0.00282 ( 43) SS BOND : angle 1.28314 ( 86) hydrogen bonds : bond 0.03776 ( 1126) hydrogen bonds : angle 5.05590 ( 3114) link_BETA1-4 : bond 0.00466 ( 18) link_BETA1-4 : angle 1.60576 ( 54) link_BETA1-6 : bond 0.00177 ( 3) link_BETA1-6 : angle 1.45180 ( 9) link_NAG-ASN : bond 0.00465 ( 43) link_NAG-ASN : angle 3.32117 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 185 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.6377 (OUTLIER) cc_final: 0.4935 (p) REVERT: A 77 ARG cc_start: 0.5586 (ttt180) cc_final: 0.5260 (tmm-80) REVERT: A 151 MET cc_start: 0.1275 (OUTLIER) cc_final: -0.0203 (pp-130) REVERT: A 188 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7562 (ttp-170) REVERT: A 235 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7191 (p90) REVERT: A 268 GLN cc_start: 0.8638 (mt0) cc_final: 0.8249 (tt0) REVERT: A 278 GLU cc_start: 0.7681 (pp20) cc_final: 0.7133 (tp30) REVERT: A 326 PHE cc_start: 0.8328 (m-80) cc_final: 0.7980 (m-10) REVERT: A 736 MET cc_start: 0.8759 (tpp) cc_final: 0.8423 (tpp) REVERT: A 810 LYS cc_start: 0.8621 (mptp) cc_final: 0.8243 (mmmt) REVERT: B 65 TRP cc_start: 0.6706 (t60) cc_final: 0.6329 (t60) REVERT: B 133 GLN cc_start: 0.8096 (tp40) cc_final: 0.7785 (mm-40) REVERT: B 151 MET cc_start: -0.0419 (OUTLIER) cc_final: -0.1892 (ttp) REVERT: B 168 TYR cc_start: 0.7342 (t80) cc_final: 0.7098 (t80) REVERT: B 235 PHE cc_start: 0.7404 (t80) cc_final: 0.6999 (t80) REVERT: B 236 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8238 (tp40) REVERT: B 361 ASP cc_start: 0.6991 (p0) cc_final: 0.6516 (t0) REVERT: B 542 LEU cc_start: 0.7712 (tt) cc_final: 0.7306 (pp) REVERT: B 554 LYS cc_start: 0.8296 (tmtt) cc_final: 0.7923 (ttmt) REVERT: B 979 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7779 (mtm110) REVERT: C 17 MET cc_start: 0.3350 (mpp) cc_final: 0.3054 (pmm) REVERT: C 151 MET cc_start: 0.3498 (pp-130) cc_final: 0.2489 (pmm) REVERT: C 198 TYR cc_start: 0.7893 (m-80) cc_final: 0.7575 (m-80) REVERT: C 199 PHE cc_start: 0.8132 (t80) cc_final: 0.7784 (t80) REVERT: C 434 ASN cc_start: 0.8059 (p0) cc_final: 0.7250 (t0) REVERT: C 464 ASP cc_start: 0.7510 (t0) cc_final: 0.7265 (t70) REVERT: C 480 LYS cc_start: 0.7262 (tttt) cc_final: 0.6772 (tptt) REVERT: C 511 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7960 (p90) REVERT: C 611 VAL cc_start: 0.9465 (p) cc_final: 0.9159 (m) REVERT: C 721 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: C 812 SER cc_start: 0.9061 (p) cc_final: 0.8617 (t) REVERT: C 975 ASP cc_start: 0.7777 (t70) cc_final: 0.6709 (m-30) REVERT: C 1069 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7655 (tttp) outliers start: 71 outliers final: 50 residues processed: 244 average time/residue: 0.1615 time to fit residues: 64.8634 Evaluate side-chains 237 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 937 THR Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 1069 LYS Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 230 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 262 optimal weight: 6.9990 chunk 209 optimal weight: 0.0570 chunk 79 optimal weight: 8.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.184040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.130554 restraints weight = 85470.289| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 4.72 r_work: 0.3302 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28422 Z= 0.116 Angle : 0.569 13.157 38791 Z= 0.276 Chirality : 0.045 0.448 4508 Planarity : 0.003 0.059 4884 Dihedral : 5.958 56.788 5006 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 3.34 % Allowed : 24.14 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.11 (0.15), residues: 3389 helix: 2.27 (0.18), residues: 811 sheet: -0.12 (0.18), residues: 798 loop : -0.88 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 979 TYR 0.025 0.001 TYR C 900 PHE 0.027 0.001 PHE C 561 TRP 0.014 0.001 TRP C 103 HIS 0.006 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00265 (28315) covalent geometry : angle 0.53444 (38513) SS BOND : bond 0.00255 ( 43) SS BOND : angle 1.09132 ( 86) hydrogen bonds : bond 0.03546 ( 1126) hydrogen bonds : angle 4.89822 ( 3114) link_BETA1-4 : bond 0.00429 ( 18) link_BETA1-4 : angle 1.55819 ( 54) link_BETA1-6 : bond 0.00199 ( 3) link_BETA1-6 : angle 1.45418 ( 9) link_NAG-ASN : bond 0.00412 ( 43) link_NAG-ASN : angle 3.19297 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.6172 (OUTLIER) cc_final: 0.4705 (p) REVERT: A 77 ARG cc_start: 0.5565 (ttt180) cc_final: 0.5174 (tmm-80) REVERT: A 151 MET cc_start: 0.1271 (OUTLIER) cc_final: -0.0265 (pp-130) REVERT: A 188 ARG cc_start: 0.7825 (ttp-170) cc_final: 0.7604 (ttp-170) REVERT: A 232 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6140 (mt) REVERT: A 235 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7154 (p90) REVERT: A 268 GLN cc_start: 0.8621 (mt0) cc_final: 0.8235 (tt0) REVERT: A 278 GLU cc_start: 0.7682 (pp20) cc_final: 0.7236 (tp30) REVERT: A 326 PHE cc_start: 0.8359 (m-80) cc_final: 0.7959 (m-10) REVERT: A 736 MET cc_start: 0.8774 (tpp) cc_final: 0.8544 (tpp) REVERT: B 65 TRP cc_start: 0.6559 (t60) cc_final: 0.6235 (t60) REVERT: B 151 MET cc_start: -0.0403 (OUTLIER) cc_final: -0.1883 (ttp) REVERT: B 236 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8235 (tp40) REVERT: B 361 ASP cc_start: 0.6957 (p0) cc_final: 0.6519 (t0) REVERT: B 520 VAL cc_start: -0.0594 (OUTLIER) cc_final: -0.0835 (p) REVERT: B 542 LEU cc_start: 0.7698 (tt) cc_final: 0.7336 (pp) REVERT: B 554 LYS cc_start: 0.8296 (tmtt) cc_final: 0.7901 (ttmt) REVERT: B 979 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7774 (mtm110) REVERT: B 988 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7770 (mm-40) REVERT: C 17 MET cc_start: 0.3417 (mpp) cc_final: 0.3172 (pmm) REVERT: C 151 MET cc_start: 0.3474 (pp-130) cc_final: 0.2376 (pmm) REVERT: C 199 PHE cc_start: 0.8127 (t80) cc_final: 0.7723 (t80) REVERT: C 434 ASN cc_start: 0.8086 (p0) cc_final: 0.7356 (t0) REVERT: C 464 ASP cc_start: 0.7471 (t0) cc_final: 0.7242 (t70) REVERT: C 480 LYS cc_start: 0.7339 (tttt) cc_final: 0.6791 (tptt) REVERT: C 611 VAL cc_start: 0.9443 (p) cc_final: 0.9132 (m) REVERT: C 721 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: C 812 SER cc_start: 0.9050 (p) cc_final: 0.8617 (t) REVERT: C 852 ASN cc_start: 0.8120 (t0) cc_final: 0.7903 (t0) REVERT: C 975 ASP cc_start: 0.7787 (t70) cc_final: 0.6729 (m-30) REVERT: C 1069 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7641 (tttp) outliers start: 61 outliers final: 47 residues processed: 232 average time/residue: 0.1665 time to fit residues: 64.5940 Evaluate side-chains 238 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 988 GLN Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 1069 LYS Chi-restraints excluded: chain C residue 1093 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 75 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 274 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 286 optimal weight: 0.9980 chunk 324 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.182282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.126513 restraints weight = 89258.277| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.89 r_work: 0.3292 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28422 Z= 0.179 Angle : 0.612 12.914 38791 Z= 0.298 Chirality : 0.046 0.490 4508 Planarity : 0.004 0.064 4884 Dihedral : 6.074 57.659 5006 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 3.61 % Allowed : 24.04 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.01 (0.15), residues: 3389 helix: 2.11 (0.18), residues: 817 sheet: -0.13 (0.19), residues: 781 loop : -0.96 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 979 TYR 0.028 0.001 TYR C 900 PHE 0.028 0.001 PHE C 561 TRP 0.015 0.001 TRP B 629 HIS 0.005 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00426 (28315) covalent geometry : angle 0.57452 (38513) SS BOND : bond 0.00284 ( 43) SS BOND : angle 1.33385 ( 86) hydrogen bonds : bond 0.03860 ( 1126) hydrogen bonds : angle 4.96116 ( 3114) link_BETA1-4 : bond 0.00387 ( 18) link_BETA1-4 : angle 1.60063 ( 54) link_BETA1-6 : bond 0.00054 ( 3) link_BETA1-6 : angle 1.64068 ( 9) link_NAG-ASN : bond 0.00382 ( 43) link_NAG-ASN : angle 3.39551 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6778 Ramachandran restraints generated. 3389 Oldfield, 0 Emsley, 3389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 175 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.6124 (OUTLIER) cc_final: 0.4634 (p) REVERT: A 77 ARG cc_start: 0.5715 (ttt180) cc_final: 0.5042 (tmm-80) REVERT: A 151 MET cc_start: 0.1343 (OUTLIER) cc_final: -0.0206 (pp-130) REVERT: A 188 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7583 (ttp-170) REVERT: A 235 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7160 (p90) REVERT: A 268 GLN cc_start: 0.8646 (mt0) cc_final: 0.8259 (tt0) REVERT: A 278 GLU cc_start: 0.7688 (pp20) cc_final: 0.7271 (tp30) REVERT: A 326 PHE cc_start: 0.8362 (m-80) cc_final: 0.7953 (m-10) REVERT: A 736 MET cc_start: 0.8745 (tpp) cc_final: 0.8489 (tpp) REVERT: A 810 LYS cc_start: 0.8621 (mptp) cc_final: 0.8288 (mmmt) REVERT: A 829 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5114 (t80) REVERT: B 65 TRP cc_start: 0.6476 (t60) cc_final: 0.6166 (t60) REVERT: B 151 MET cc_start: -0.0377 (OUTLIER) cc_final: -0.1908 (ttp) REVERT: B 236 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8246 (tp40) REVERT: B 361 ASP cc_start: 0.7000 (p0) cc_final: 0.6577 (t0) REVERT: B 520 VAL cc_start: -0.0562 (OUTLIER) cc_final: -0.0807 (p) REVERT: B 542 LEU cc_start: 0.7679 (tt) cc_final: 0.7298 (pp) REVERT: B 554 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7858 (ttmt) REVERT: B 979 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7807 (mtm110) REVERT: C 151 MET cc_start: 0.3410 (pp-130) cc_final: 0.2426 (pmm) REVERT: C 199 PHE cc_start: 0.8226 (t80) cc_final: 0.7815 (t80) REVERT: C 434 ASN cc_start: 0.8109 (p0) cc_final: 0.7409 (t0) REVERT: C 464 ASP cc_start: 0.7578 (t0) cc_final: 0.7324 (t70) REVERT: C 480 LYS cc_start: 0.7416 (tttt) cc_final: 0.6739 (tptt) REVERT: C 611 VAL cc_start: 0.9451 (p) cc_final: 0.9145 (m) REVERT: C 721 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: C 812 SER cc_start: 0.9064 (p) cc_final: 0.8603 (t) REVERT: C 852 ASN cc_start: 0.8202 (t0) cc_final: 0.7951 (t0) REVERT: C 975 ASP cc_start: 0.7796 (t70) cc_final: 0.6763 (m-30) REVERT: C 1069 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7674 (tttp) outliers start: 69 outliers final: 53 residues processed: 230 average time/residue: 0.1673 time to fit residues: 63.8124 Evaluate side-chains 234 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 172 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 621 HIS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 829 PHE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 937 THR Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1102 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 658 CYS Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain C residue 736 MET Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 1069 LYS Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 152 optimal weight: 0.5980 chunk 325 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 306 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 236 optimal weight: 0.0000 chunk 233 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 36 optimal weight: 40.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 849 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 = 0.4348 r_free = 0.4348 target = 0.185274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126033 restraints weight = 70531.694| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.46 r_work: 0.3391 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28422 Z= 0.098 Angle : 0.563 12.275 38791 Z= 0.274 Chirality : 0.044 0.419 4508 Planarity : 0.003 0.062 4884 Dihedral : 5.823 56.995 5006 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 3.11 % Allowed : 24.67 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.18 (0.15), residues: 3389 helix: 2.35 (0.18), residues: 814 sheet: -0.03 (0.19), residues: 786 loop : -0.88 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 843 TYR 0.022 0.001 TYR B 900 PHE 0.028 0.001 PHE C 561 TRP 0.013 0.001 TRP A 629 HIS 0.004 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00213 (28315) covalent geometry : angle 0.52880 (38513) SS BOND : bond 0.00234 ( 43) SS BOND : angle 0.96819 ( 86) hydrogen bonds : bond 0.03339 ( 1126) hydrogen bonds : angle 4.78677 ( 3114) link_BETA1-4 : bond 0.00498 ( 18) link_BETA1-4 : angle 1.45836 ( 54) link_BETA1-6 : bond 0.00230 ( 3) link_BETA1-6 : angle 1.38785 ( 9) link_NAG-ASN : bond 0.00465 ( 43) link_NAG-ASN : angle 3.17236 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8144.89 seconds wall clock time: 139 minutes 52.12 seconds (8392.12 seconds total)