Starting phenix.real_space_refine on Sun Aug 24 04:18:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d7h_46605/08_2025/9d7h_46605.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d7h_46605/08_2025/9d7h_46605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d7h_46605/08_2025/9d7h_46605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d7h_46605/08_2025/9d7h_46605.map" model { file = "/net/cci-nas-00/data/ceres_data/9d7h_46605/08_2025/9d7h_46605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d7h_46605/08_2025/9d7h_46605.cif" } resolution = 3.59 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= -0.000 sd= 0.031 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 115 5.16 5 C 10605 2.51 5 N 2828 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16948 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3403 Classifications: {'peptide': 432} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3365 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 4 Chain: "D" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1008 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "E" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3447 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "F" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1447 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 175} Chain breaks: 5 Chain: "H" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1189 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: 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: "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 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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 Time building chain proxies: 4.21, per 1000 atoms: 0.25 Number of scatterers: 16948 At special positions: 0 Unit cell: (131.76, 167.4, 126.36, 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 115 16.00 O 3400 8.00 N 2828 7.00 C 10605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 378 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 355 " " NAG A 606 " - " ASN A 386 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 448 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 295 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 355 " " NAG C 608 " - " ASN C 392 " " NAG C 609 " - " ASN C 448 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 355 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 448 " " NAG E 604 " - " ASN E 133 " " NAG E 605 " - " ASN E 137 " " NAG E 606 " - " ASN E 234 " " NAG E 607 " - " ASN E 301 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG I 1 " - " ASN A 148 " " NAG J 1 " - " ASN A 152 " " NAG K 1 " - " ASN A 197 " " NAG L 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 295 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 363 " " NAG Q 1 " - " ASN C 133 " " NAG R 1 " - " ASN C 148 " " NAG S 1 " - " ASN C 152 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN E 363 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 88 " " NAG b 1 " - " ASN E 148 " " NAG c 1 " - " ASN E 152 " " NAG d 1 " - " ASN E 262 " " NAG e 1 " - " ASN E 276 " " NAG f 1 " - " ASN E 295 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 606.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 34 sheets defined 18.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.882A pdb=" N ARG A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 480 removed outlier: 4.013A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.589A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.802A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 641 through 661 removed outlier: 3.850A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.852A pdb=" N ARG C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.579A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 541 removed outlier: 4.361A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 536 through 541' Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 569 through 596 removed outlier: 4.117A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 593 " --> pdb=" O ASP D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.504A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 632 Processing helix chain 'D' and resid 638 through 662 removed outlier: 3.542A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 662 " --> pdb=" O GLN D 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.400A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.600A pdb=" N THR E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.846A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.565A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.602A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.659A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 659 removed outlier: 3.740A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.964A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.007A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 11.499A pdb=" N LYS A 487 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASP A 47 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 489 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N TRP A 45 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ILE A 491 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.817A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.553A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 169 Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 287 current: chain 'A' and resid 315 through 322 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 322 current: chain 'A' and resid 394 through 395 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 394 through 395 current: chain 'A' and resid 465 through 470 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 382 through 385 removed outlier: 4.488A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA8, first strand: chain 'C' and resid 495 through 499 removed outlier: 4.210A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.722A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 86 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR C 244 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C 84 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 3.649A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AB4, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB5, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 329 through 334 removed outlier: 3.589A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB7, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.554A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.558A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.277A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.994A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.138A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.581A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 161 through 169 removed outlier: 3.940A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 302 removed outlier: 7.319A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 331 through 334 current: chain 'E' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 393 through 395 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC6, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.575A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 374 through 377 removed outlier: 3.501A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AC9, first strand: chain 'G' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 9 through 13 current: chain 'G' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 48 current: chain 'G' and resid 96 through 98 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 19 through 23 removed outlier: 3.513A pdb=" N ALA G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 114 through 118 removed outlier: 3.635A pdb=" N LEU G 135 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE G 118 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL G 133 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR G 172 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 145 through 149 removed outlier: 3.828A pdb=" N SER G 192 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS G 204 " --> pdb=" O CYS G 193 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.528A pdb=" N GLN H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.301A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 164 through 165 removed outlier: 3.694A pdb=" N HIS H 164 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL H 181 " --> pdb=" O HIS H 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'H' and resid 169 through 170 removed outlier: 3.784A pdb=" N SER H 177 " --> pdb=" O VAL H 169 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1221 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: 2.53 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5271 1.34 - 1.47: 4419 1.47 - 1.60: 7433 1.60 - 1.73: 0 1.73 - 1.86: 151 Bond restraints: 17274 Sorted by residual: bond pdb=" C ASP C 78 " pdb=" N PRO C 79 " ideal model delta sigma weight residual 1.334 1.419 -0.085 2.34e-02 1.83e+03 1.32e+01 bond pdb=" CA ASN A 136 " pdb=" CB ASN A 136 " ideal model delta sigma weight residual 1.524 1.569 -0.045 1.53e-02 4.27e+03 8.47e+00 bond pdb=" C1 NAG C 604 " pdb=" O5 NAG C 604 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.98e+00 bond pdb=" N ASN G 170 " pdb=" CA ASN G 170 " ideal model delta sigma weight residual 1.460 1.499 -0.038 1.51e-02 4.39e+03 6.50e+00 bond pdb=" C1 NAG B 702 " pdb=" O5 NAG B 702 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 17269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 22889 2.68 - 5.36: 471 5.36 - 8.04: 81 8.04 - 10.72: 12 10.72 - 13.40: 8 Bond angle restraints: 23461 Sorted by residual: angle pdb=" C ASN G 169 " pdb=" N ASN G 170 " pdb=" CA ASN G 170 " ideal model delta sigma weight residual 122.36 133.83 -11.47 1.42e+00 4.96e-01 6.52e+01 angle pdb=" C ASN A 377 " pdb=" N CYS A 378 " pdb=" CA CYS A 378 " ideal model delta sigma weight residual 122.65 114.71 7.94 1.49e+00 4.50e-01 2.84e+01 angle pdb=" CA PRO C 76 " pdb=" N PRO C 76 " pdb=" CD PRO C 76 " ideal model delta sigma weight residual 112.00 104.57 7.43 1.40e+00 5.10e-01 2.82e+01 angle pdb=" CA ASN G 170 " pdb=" CB ASN G 170 " pdb=" CG ASN G 170 " ideal model delta sigma weight residual 112.60 117.78 -5.18 1.00e+00 1.00e+00 2.68e+01 angle pdb=" CB LYS A 207 " pdb=" CG LYS A 207 " pdb=" CD LYS A 207 " ideal model delta sigma weight residual 111.30 123.14 -11.84 2.30e+00 1.89e-01 2.65e+01 ... (remaining 23456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 10543 21.87 - 43.74: 703 43.74 - 65.61: 116 65.61 - 87.47: 65 87.47 - 109.34: 32 Dihedral angle restraints: 11459 sinusoidal: 5652 harmonic: 5807 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -169.52 83.52 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -3.39 -82.61 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 378 " pdb=" CB CYS A 378 " ideal model delta sinusoidal sigma weight residual -86.00 -162.20 76.20 1 1.00e+01 1.00e-02 7.31e+01 ... (remaining 11456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2764 0.118 - 0.235: 123 0.235 - 0.353: 14 0.353 - 0.470: 5 0.470 - 0.588: 1 Chirality restraints: 2907 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A 295 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.64e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN E 152 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C2 NAG a 2 " pdb=" C1 NAG a 2 " pdb=" C3 NAG a 2 " pdb=" N2 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 2904 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 78 " -0.041 2.00e-02 2.50e+03 7.92e-02 6.28e+01 pdb=" C ASP C 78 " 0.137 2.00e-02 2.50e+03 pdb=" O ASP C 78 " -0.052 2.00e-02 2.50e+03 pdb=" N PRO C 79 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 78 " 0.038 2.00e-02 2.50e+03 7.43e-02 5.51e+01 pdb=" C ASP E 78 " -0.128 2.00e-02 2.50e+03 pdb=" O ASP E 78 " 0.049 2.00e-02 2.50e+03 pdb=" N PRO E 79 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 135 " -0.034 2.00e-02 2.50e+03 6.79e-02 4.61e+01 pdb=" C THR E 135 " 0.117 2.00e-02 2.50e+03 pdb=" O THR E 135 " -0.045 2.00e-02 2.50e+03 pdb=" N ASN E 136 " -0.038 2.00e-02 2.50e+03 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3757 2.79 - 3.32: 13798 3.32 - 3.85: 26282 3.85 - 4.37: 28375 4.37 - 4.90: 51484 Nonbonded interactions: 123696 Sorted by model distance: nonbonded pdb=" O LEU E 369 " pdb=" OG1 THR E 373 " model vdw 2.267 3.040 nonbonded pdb=" O VAL C 36 " pdb=" OG1 THR D 606 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR E 303 " pdb=" O ASP E 321A" model vdw 2.308 3.040 nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.317 3.040 nonbonded pdb=" O ILE D 635 " pdb=" OG1 THR D 639 " model vdw 2.317 3.040 ... (remaining 123691 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 34 through 56 or resid 67 through 135 or resid 144 through \ 396 or resid 412 through 607)) selection = (chain 'C' and (resid 34 through 77 or resid 82 through 177 or resid 189 through \ 396 or resid 412 through 607)) selection = (chain 'E' and (resid 34 through 56 or resid 67 through 77 or resid 82 through 1 \ 35 or resid 144 through 177 or resid 189 through 396 or resid 412 through 607)) } ncs_group { reference = (chain 'B' and resid 521 through 701) selection = (chain 'D' and (resid 521 through 546 or resid 569 through 701)) selection = (chain 'F' and resid 521 through 701) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' } ncs_group { reference = chain 'L' selection = chain 'R' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.750 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.006 0.106 17393 Z= 0.284 Angle : 1.028 16.751 23783 Z= 0.495 Chirality : 0.062 0.588 2907 Planarity : 0.008 0.127 2866 Dihedral : 16.052 109.343 7594 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.17), residues: 1960 helix: -1.23 (0.24), residues: 353 sheet: -0.93 (0.21), residues: 618 loop : -1.94 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 588 TYR 0.016 0.001 TYR H 145 PHE 0.029 0.002 PHE G 118 TRP 0.027 0.002 TRP C 35 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00601 (17274) covalent geometry : angle 0.96774 (23461) SS BOND : bond 0.00718 ( 35) SS BOND : angle 3.71083 ( 70) hydrogen bonds : bond 0.20488 ( 434) hydrogen bonds : angle 8.22765 ( 1221) link_BETA1-4 : bond 0.00887 ( 31) link_BETA1-4 : angle 3.08182 ( 93) link_NAG-ASN : bond 0.00427 ( 53) link_NAG-ASN : angle 2.87213 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8406 (mmmt) cc_final: 0.7767 (tmtt) REVERT: A 231 LYS cc_start: 0.8292 (mtmm) cc_final: 0.8026 (mtmm) REVERT: A 268 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7359 (mt-10) REVERT: B 652 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7767 (tm-30) REVERT: C 172 ASP cc_start: 0.8887 (p0) cc_final: 0.8661 (p0) REVERT: E 99 ASN cc_start: 0.8591 (t0) cc_final: 0.8231 (t0) REVERT: F 648 GLU cc_start: 0.8368 (tt0) cc_final: 0.8098 (tt0) outliers start: 1 outliers final: 1 residues processed: 252 average time/residue: 0.1328 time to fit residues: 50.7477 Evaluate side-chains 211 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN C 99 ASN E 411 ASN F 630 GLN F 650 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.140073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108067 restraints weight = 27865.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110894 restraints weight = 19469.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111447 restraints weight = 13284.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112302 restraints weight = 12129.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112783 restraints weight = 11265.638| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17393 Z= 0.154 Angle : 0.670 9.806 23783 Z= 0.320 Chirality : 0.046 0.427 2907 Planarity : 0.005 0.083 2866 Dihedral : 10.810 68.111 3890 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.96 % Allowed : 7.37 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.18), residues: 1960 helix: 0.31 (0.28), residues: 358 sheet: -0.65 (0.22), residues: 594 loop : -1.67 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.011 0.001 TYR H 50 PHE 0.017 0.001 PHE H 52 TRP 0.015 0.001 TRP C 35 HIS 0.003 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00363 (17274) covalent geometry : angle 0.61981 (23461) SS BOND : bond 0.00489 ( 35) SS BOND : angle 2.31297 ( 70) hydrogen bonds : bond 0.04151 ( 434) hydrogen bonds : angle 5.43709 ( 1221) link_BETA1-4 : bond 0.00559 ( 31) link_BETA1-4 : angle 2.38131 ( 93) link_NAG-ASN : bond 0.00335 ( 53) link_NAG-ASN : angle 2.17101 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 0.706 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 231 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7897 (mtmm) REVERT: A 268 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6900 (mt-10) REVERT: A 377 ASN cc_start: 0.8457 (t0) cc_final: 0.8142 (t0) REVERT: B 621 GLU cc_start: 0.7426 (pp20) cc_final: 0.6872 (pp20) REVERT: E 99 ASN cc_start: 0.8436 (t0) cc_final: 0.8035 (t0) REVERT: F 590 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8341 (mm-40) REVERT: G 171 LYS cc_start: 0.7227 (tptm) cc_final: 0.6906 (tptm) REVERT: G 180 LEU cc_start: 0.8451 (mt) cc_final: 0.7959 (mt) outliers start: 17 outliers final: 14 residues processed: 250 average time/residue: 0.1375 time to fit residues: 51.8702 Evaluate side-chains 230 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 49 optimal weight: 2.9990 chunk 174 optimal weight: 0.0470 chunk 187 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 177 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 302 ASN A 478 ASN C 428 GLN E 348 GLN F 653 GLN G 169 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096460 restraints weight = 27372.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099259 restraints weight = 20554.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.100138 restraints weight = 14532.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.100717 restraints weight = 12585.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100965 restraints weight = 11549.321| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17393 Z= 0.185 Angle : 0.678 9.691 23783 Z= 0.322 Chirality : 0.047 0.458 2907 Planarity : 0.004 0.069 2866 Dihedral : 8.671 59.611 3888 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.63 % Allowed : 10.80 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.19), residues: 1960 helix: 0.84 (0.29), residues: 364 sheet: -0.65 (0.21), residues: 600 loop : -1.54 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 503 TYR 0.021 0.001 TYR G 140 PHE 0.027 0.002 PHE G 139 TRP 0.017 0.001 TRP B 571 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00443 (17274) covalent geometry : angle 0.63049 (23461) SS BOND : bond 0.00502 ( 35) SS BOND : angle 2.36240 ( 70) hydrogen bonds : bond 0.04145 ( 434) hydrogen bonds : angle 4.97908 ( 1221) link_BETA1-4 : bond 0.00576 ( 31) link_BETA1-4 : angle 2.33615 ( 93) link_NAG-ASN : bond 0.00344 ( 53) link_NAG-ASN : angle 2.09074 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.8289 (mtmm) cc_final: 0.7967 (mtmm) REVERT: A 268 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7103 (mt-10) REVERT: A 302 ASN cc_start: 0.8753 (m110) cc_final: 0.8491 (m-40) REVERT: A 377 ASN cc_start: 0.8666 (t0) cc_final: 0.8278 (t0) REVERT: A 444 ARG cc_start: 0.8082 (tpt170) cc_final: 0.7870 (tpt170) REVERT: B 621 GLU cc_start: 0.7682 (pp20) cc_final: 0.7087 (pp20) REVERT: C 102 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7308 (tm-30) REVERT: D 603 ILE cc_start: 0.8773 (mp) cc_final: 0.8537 (tt) REVERT: E 99 ASN cc_start: 0.8446 (t0) cc_final: 0.8028 (t0) REVERT: E 153 MET cc_start: 0.8315 (mmm) cc_final: 0.7899 (tpt) REVERT: F 590 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8321 (mm-40) REVERT: F 632 ASP cc_start: 0.8401 (t70) cc_final: 0.8092 (t70) REVERT: G 171 LYS cc_start: 0.7309 (tptm) cc_final: 0.7028 (tptm) outliers start: 29 outliers final: 24 residues processed: 240 average time/residue: 0.1450 time to fit residues: 52.2675 Evaluate side-chains 239 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain G residue 110 LYS Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 179 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 190 optimal weight: 0.8980 chunk 145 optimal weight: 0.0870 chunk 110 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN C 85 HIS F 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094839 restraints weight = 27453.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097704 restraints weight = 21264.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098733 restraints weight = 15115.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099116 restraints weight = 13098.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.099345 restraints weight = 12090.440| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17393 Z= 0.207 Angle : 0.682 9.783 23783 Z= 0.326 Chirality : 0.047 0.460 2907 Planarity : 0.004 0.059 2866 Dihedral : 7.724 59.920 3888 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.47 % Allowed : 12.88 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.19), residues: 1960 helix: 1.16 (0.30), residues: 356 sheet: -0.63 (0.22), residues: 595 loop : -1.50 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 189 TYR 0.027 0.002 TYR G 140 PHE 0.015 0.002 PHE H 52 TRP 0.019 0.001 TRP B 571 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00497 (17274) covalent geometry : angle 0.63579 (23461) SS BOND : bond 0.00506 ( 35) SS BOND : angle 2.38396 ( 70) hydrogen bonds : bond 0.04053 ( 434) hydrogen bonds : angle 4.83918 ( 1221) link_BETA1-4 : bond 0.00567 ( 31) link_BETA1-4 : angle 2.24172 ( 93) link_NAG-ASN : bond 0.00375 ( 53) link_NAG-ASN : angle 2.13945 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8651 (t0) cc_final: 0.8255 (t0) REVERT: B 621 GLU cc_start: 0.7547 (pp20) cc_final: 0.6954 (pp20) REVERT: B 661 LEU cc_start: 0.9074 (mt) cc_final: 0.8582 (tp) REVERT: C 102 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7370 (tm-30) REVERT: E 99 ASN cc_start: 0.8477 (t0) cc_final: 0.8023 (t0) REVERT: F 590 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8266 (mm-40) REVERT: F 632 ASP cc_start: 0.8419 (t70) cc_final: 0.8146 (t70) outliers start: 44 outliers final: 32 residues processed: 254 average time/residue: 0.1353 time to fit residues: 52.0689 Evaluate side-chains 247 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 179 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 62 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN F 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095589 restraints weight = 27215.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.097155 restraints weight = 20242.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.097979 restraints weight = 17032.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.098840 restraints weight = 13948.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.098911 restraints weight = 12595.259| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17393 Z= 0.168 Angle : 0.649 9.664 23783 Z= 0.310 Chirality : 0.046 0.429 2907 Planarity : 0.004 0.053 2866 Dihedral : 7.485 59.930 3888 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.53 % Allowed : 13.72 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.19), residues: 1960 helix: 1.26 (0.30), residues: 357 sheet: -0.63 (0.22), residues: 591 loop : -1.47 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 189 TYR 0.019 0.001 TYR G 140 PHE 0.012 0.001 PHE H 78 TRP 0.018 0.001 TRP B 571 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00402 (17274) covalent geometry : angle 0.60383 (23461) SS BOND : bond 0.00450 ( 35) SS BOND : angle 2.34185 ( 70) hydrogen bonds : bond 0.03732 ( 434) hydrogen bonds : angle 4.68007 ( 1221) link_BETA1-4 : bond 0.00580 ( 31) link_BETA1-4 : angle 2.13896 ( 93) link_NAG-ASN : bond 0.00330 ( 53) link_NAG-ASN : angle 2.01085 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8587 (t0) cc_final: 0.8351 (t0) REVERT: B 621 GLU cc_start: 0.7656 (pp20) cc_final: 0.7075 (pp20) REVERT: B 661 LEU cc_start: 0.9086 (mt) cc_final: 0.8576 (tp) REVERT: C 102 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7341 (tm-30) REVERT: E 99 ASN cc_start: 0.8439 (t0) cc_final: 0.7973 (t0) REVERT: E 377 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7969 (p0) REVERT: F 590 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8242 (mm-40) REVERT: F 632 ASP cc_start: 0.8407 (t70) cc_final: 0.8127 (t70) outliers start: 45 outliers final: 33 residues processed: 246 average time/residue: 0.1322 time to fit residues: 49.5192 Evaluate side-chains 248 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 170 ASN Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 179 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 136 ASN F 656 ASN G 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.122598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094286 restraints weight = 27469.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.096803 restraints weight = 22200.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.097186 restraints weight = 16309.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.097709 restraints weight = 15139.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.098069 restraints weight = 13591.957| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17393 Z= 0.200 Angle : 0.681 11.469 23783 Z= 0.323 Chirality : 0.047 0.464 2907 Planarity : 0.004 0.052 2866 Dihedral : 7.417 59.858 3888 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.09 % Allowed : 14.62 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.19), residues: 1960 helix: 1.28 (0.30), residues: 357 sheet: -0.64 (0.22), residues: 570 loop : -1.47 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 189 TYR 0.021 0.001 TYR G 140 PHE 0.012 0.001 PHE G 49 TRP 0.021 0.001 TRP B 571 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00482 (17274) covalent geometry : angle 0.63750 (23461) SS BOND : bond 0.00501 ( 35) SS BOND : angle 2.41250 ( 70) hydrogen bonds : bond 0.03871 ( 434) hydrogen bonds : angle 4.67439 ( 1221) link_BETA1-4 : bond 0.00561 ( 31) link_BETA1-4 : angle 2.13141 ( 93) link_NAG-ASN : bond 0.00349 ( 53) link_NAG-ASN : angle 2.05322 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.7412 (pp20) cc_final: 0.6832 (pp20) REVERT: B 661 LEU cc_start: 0.9139 (mt) cc_final: 0.8647 (tp) REVERT: C 102 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7444 (tm-30) REVERT: E 99 ASN cc_start: 0.8475 (t0) cc_final: 0.8018 (t0) REVERT: E 271 MET cc_start: 0.7904 (mpp) cc_final: 0.7682 (mpp) REVERT: E 377 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7920 (p0) REVERT: F 540 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7323 (mt0) REVERT: F 590 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8254 (mm-40) REVERT: F 632 ASP cc_start: 0.8500 (t70) cc_final: 0.8274 (t70) outliers start: 55 outliers final: 40 residues processed: 255 average time/residue: 0.1305 time to fit residues: 50.6653 Evaluate side-chains 253 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 179 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 55 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 85 HIS ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN F 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093910 restraints weight = 27408.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.095870 restraints weight = 20934.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.097031 restraints weight = 15784.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.097895 restraints weight = 13860.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098111 restraints weight = 12818.401| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17393 Z= 0.198 Angle : 0.685 9.899 23783 Z= 0.328 Chirality : 0.047 0.448 2907 Planarity : 0.004 0.050 2866 Dihedral : 7.425 59.840 3888 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.92 % Allowed : 14.96 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.19), residues: 1960 helix: 1.28 (0.30), residues: 358 sheet: -0.65 (0.22), residues: 570 loop : -1.47 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 189 TYR 0.019 0.001 TYR G 140 PHE 0.012 0.001 PHE G 49 TRP 0.021 0.001 TRP B 571 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00478 (17274) covalent geometry : angle 0.64281 (23461) SS BOND : bond 0.00495 ( 35) SS BOND : angle 2.40371 ( 70) hydrogen bonds : bond 0.03835 ( 434) hydrogen bonds : angle 4.66483 ( 1221) link_BETA1-4 : bond 0.00568 ( 31) link_BETA1-4 : angle 2.10520 ( 93) link_NAG-ASN : bond 0.00337 ( 53) link_NAG-ASN : angle 2.02801 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7718 (mmm160) REVERT: B 621 GLU cc_start: 0.7619 (pp20) cc_final: 0.7017 (pp20) REVERT: B 661 LEU cc_start: 0.9156 (mt) cc_final: 0.8654 (tp) REVERT: C 102 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 145 GLU cc_start: 0.5192 (pm20) cc_final: 0.4725 (pm20) REVERT: D 633 LYS cc_start: 0.7835 (pttp) cc_final: 0.7440 (pttt) REVERT: E 99 ASN cc_start: 0.8478 (t0) cc_final: 0.8004 (t0) REVERT: E 271 MET cc_start: 0.7939 (mpp) cc_final: 0.7698 (mpp) REVERT: E 377 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7932 (p0) REVERT: E 500 ARG cc_start: 0.6764 (mmt180) cc_final: 0.6386 (mmt180) REVERT: F 540 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: F 590 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8241 (mm-40) REVERT: F 632 ASP cc_start: 0.8516 (t70) cc_final: 0.8273 (t70) outliers start: 52 outliers final: 43 residues processed: 257 average time/residue: 0.1372 time to fit residues: 53.5956 Evaluate side-chains 254 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 179 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 24 optimal weight: 0.4980 chunk 192 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 191 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 ASN F 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093487 restraints weight = 27530.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.095880 restraints weight = 20145.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.096768 restraints weight = 14592.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097190 restraints weight = 13594.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097478 restraints weight = 12327.275| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17393 Z= 0.190 Angle : 0.682 9.796 23783 Z= 0.326 Chirality : 0.047 0.453 2907 Planarity : 0.004 0.049 2866 Dihedral : 7.379 59.988 3888 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.76 % Allowed : 15.58 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.19), residues: 1960 helix: 1.39 (0.30), residues: 352 sheet: -0.66 (0.22), residues: 570 loop : -1.49 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 189 TYR 0.022 0.001 TYR G 140 PHE 0.018 0.002 PHE H 146 TRP 0.021 0.001 TRP B 571 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00458 (17274) covalent geometry : angle 0.63902 (23461) SS BOND : bond 0.00509 ( 35) SS BOND : angle 2.41719 ( 70) hydrogen bonds : bond 0.03799 ( 434) hydrogen bonds : angle 4.63769 ( 1221) link_BETA1-4 : bond 0.00559 ( 31) link_BETA1-4 : angle 2.08502 ( 93) link_NAG-ASN : bond 0.00333 ( 53) link_NAG-ASN : angle 2.04554 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ARG cc_start: 0.8074 (mmm160) cc_final: 0.7730 (mmm160) REVERT: B 621 GLU cc_start: 0.7605 (pp20) cc_final: 0.6994 (pp20) REVERT: B 661 LEU cc_start: 0.9139 (mt) cc_final: 0.8655 (tp) REVERT: C 102 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 145 GLU cc_start: 0.4984 (pm20) cc_final: 0.4259 (pm20) REVERT: D 633 LYS cc_start: 0.7937 (pttp) cc_final: 0.7638 (pttp) REVERT: E 271 MET cc_start: 0.7985 (mpp) cc_final: 0.7759 (mpp) REVERT: E 377 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7938 (p0) REVERT: E 500 ARG cc_start: 0.6765 (mmt180) cc_final: 0.6554 (mmt180) REVERT: F 540 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7268 (mt0) REVERT: F 590 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8244 (mm-40) REVERT: F 632 ASP cc_start: 0.8550 (t70) cc_final: 0.8317 (t70) REVERT: H 105 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.7411 (mtp-110) outliers start: 49 outliers final: 41 residues processed: 240 average time/residue: 0.1330 time to fit residues: 48.4259 Evaluate side-chains 249 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 172 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.095644 restraints weight = 27282.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.099341 restraints weight = 18091.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099977 restraints weight = 12787.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.100226 restraints weight = 11165.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100310 restraints weight = 10583.478| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17393 Z= 0.138 Angle : 0.642 10.184 23783 Z= 0.306 Chirality : 0.046 0.427 2907 Planarity : 0.003 0.048 2866 Dihedral : 7.096 59.797 3888 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.42 % Allowed : 15.97 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.19), residues: 1960 helix: 1.55 (0.31), residues: 351 sheet: -0.56 (0.22), residues: 577 loop : -1.45 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 189 TYR 0.021 0.001 TYR G 140 PHE 0.018 0.001 PHE H 146 TRP 0.040 0.001 TRP G 148 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00329 (17274) covalent geometry : angle 0.60275 (23461) SS BOND : bond 0.00399 ( 35) SS BOND : angle 2.14933 ( 70) hydrogen bonds : bond 0.03352 ( 434) hydrogen bonds : angle 4.46624 ( 1221) link_BETA1-4 : bond 0.00560 ( 31) link_BETA1-4 : angle 1.97302 ( 93) link_NAG-ASN : bond 0.00281 ( 53) link_NAG-ASN : angle 1.92587 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.7537 (pp20) cc_final: 0.6900 (pp20) REVERT: B 661 LEU cc_start: 0.9125 (mt) cc_final: 0.8636 (tp) REVERT: C 102 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7321 (tm-30) REVERT: C 145 GLU cc_start: 0.5120 (pm20) cc_final: 0.4376 (pm20) REVERT: D 603 ILE cc_start: 0.8851 (mp) cc_final: 0.8536 (tt) REVERT: E 99 ASN cc_start: 0.8372 (t0) cc_final: 0.7901 (t0) REVERT: E 199 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8590 (p) REVERT: E 271 MET cc_start: 0.7940 (mpp) cc_final: 0.7697 (mpp) REVERT: E 326 ILE cc_start: 0.9278 (mm) cc_final: 0.9039 (mm) REVERT: E 500 ARG cc_start: 0.6732 (mmt180) cc_final: 0.6468 (mmt180) REVERT: F 540 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7177 (mt0) REVERT: F 590 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8225 (mm-40) REVERT: F 632 ASP cc_start: 0.8496 (t70) cc_final: 0.8266 (t70) REVERT: H 105 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.7419 (mtp-110) outliers start: 43 outliers final: 36 residues processed: 250 average time/residue: 0.1346 time to fit residues: 50.8547 Evaluate side-chains 249 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 69 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 112 optimal weight: 0.0670 chunk 6 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN E 136 ASN F 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.125329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.096746 restraints weight = 27116.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099301 restraints weight = 19311.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100365 restraints weight = 14090.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.100700 restraints weight = 12402.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.100973 restraints weight = 11518.346| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17393 Z= 0.113 Angle : 0.628 10.791 23783 Z= 0.298 Chirality : 0.046 0.489 2907 Planarity : 0.003 0.047 2866 Dihedral : 6.919 59.340 3888 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.86 % Allowed : 16.82 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.19), residues: 1960 helix: 1.74 (0.31), residues: 348 sheet: -0.46 (0.21), residues: 599 loop : -1.41 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 444 TYR 0.021 0.001 TYR G 140 PHE 0.018 0.001 PHE H 146 TRP 0.046 0.001 TRP G 148 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00263 (17274) covalent geometry : angle 0.58888 (23461) SS BOND : bond 0.00355 ( 35) SS BOND : angle 2.00428 ( 70) hydrogen bonds : bond 0.03125 ( 434) hydrogen bonds : angle 4.36125 ( 1221) link_BETA1-4 : bond 0.00589 ( 31) link_BETA1-4 : angle 1.92417 ( 93) link_NAG-ASN : bond 0.00389 ( 53) link_NAG-ASN : angle 1.99531 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 661 LEU cc_start: 0.9104 (mt) cc_final: 0.8618 (tp) REVERT: C 102 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7253 (tm-30) REVERT: C 145 GLU cc_start: 0.5070 (pm20) cc_final: 0.4326 (pm20) REVERT: D 641 ILE cc_start: 0.8112 (mm) cc_final: 0.7881 (pt) REVERT: E 99 ASN cc_start: 0.8330 (t0) cc_final: 0.7878 (t0) REVERT: E 199 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8705 (p) REVERT: E 271 MET cc_start: 0.7912 (mpp) cc_final: 0.7677 (mpp) REVERT: E 326 ILE cc_start: 0.9286 (mm) cc_final: 0.8905 (mm) REVERT: E 500 ARG cc_start: 0.6705 (mmt180) cc_final: 0.6432 (mmt180) REVERT: F 540 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7175 (mt0) REVERT: H 105 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.7382 (mtp-110) outliers start: 33 outliers final: 26 residues processed: 248 average time/residue: 0.1386 time to fit residues: 52.0441 Evaluate side-chains 241 residues out of total 1780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 36 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 129 optimal weight: 0.0980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 377 ASN F 656 ASN G 169 ASN G 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.097310 restraints weight = 27097.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.099814 restraints weight = 18932.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.100701 restraints weight = 14534.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.101168 restraints weight = 13238.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101275 restraints weight = 12170.538| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17393 Z= 0.121 Angle : 0.642 10.582 23783 Z= 0.306 Chirality : 0.046 0.484 2907 Planarity : 0.003 0.047 2866 Dihedral : 6.827 59.375 3888 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.14 % Allowed : 16.93 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.19), residues: 1960 helix: 1.76 (0.31), residues: 348 sheet: -0.44 (0.21), residues: 602 loop : -1.41 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 189 TYR 0.020 0.001 TYR G 140 PHE 0.018 0.001 PHE H 146 TRP 0.043 0.001 TRP G 148 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00282 (17274) covalent geometry : angle 0.60473 (23461) SS BOND : bond 0.00353 ( 35) SS BOND : angle 1.96713 ( 70) hydrogen bonds : bond 0.03102 ( 434) hydrogen bonds : angle 4.33815 ( 1221) link_BETA1-4 : bond 0.00596 ( 31) link_BETA1-4 : angle 1.91380 ( 93) link_NAG-ASN : bond 0.00354 ( 53) link_NAG-ASN : angle 1.97767 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.04 seconds wall clock time: 47 minutes 6.94 seconds (2826.94 seconds total)