Starting phenix.real_space_refine on Tue Apr 7 16:29:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ld1_23279/04_2026/7ld1_23279.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ld1_23279/04_2026/7ld1_23279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ld1_23279/04_2026/7ld1_23279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ld1_23279/04_2026/7ld1_23279.map" model { file = "/net/cci-nas-00/data/ceres_data/7ld1_23279/04_2026/7ld1_23279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ld1_23279/04_2026/7ld1_23279.cif" } resolution = 3.4 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 18478 2.51 5 N 5018 2.21 5 O 5833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29444 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7046 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "B" Number of atoms: 7046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7046 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7026 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 518 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 12, 'GLU:plan': 12, 'GLN:plan1': 7, 'ARG:plan': 4, 'PHE:plan': 5, 'TYR:plan': 9, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 264 Chain: "M" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1248 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 526 Unresolved non-hydrogen angles: 687 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 6, 'ASN:plan1': 7, 'PHE:plan': 5, 'HIS:plan': 4, 'TYR:plan': 9, 'TRP:plan': 4, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 282 Chain: "N" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1245 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 485 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 8, 'GLN:plan1': 10, 'TYR:plan': 8, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'ASN:plan1': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 290 Chain: "P" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1235 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 539 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 6, 'ASN:plan1': 7, 'PHE:plan': 5, 'HIS:plan': 4, 'TYR:plan': 9, 'TRP:plan': 4, 'ARG:plan': 6, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 291 Chain: "O" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1235 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 9, 'GLN:plan1': 11, 'TYR:plan': 8, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'ASN:plan1': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 299 Chain: "H" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1235 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 539 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 6, 'ASN:plan1': 7, 'PHE:plan': 5, 'HIS:plan': 4, 'TYR:plan': 9, 'TRP:plan': 4, 'ARG:plan': 6, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 291 Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1229 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 9, 'GLN:plan1': 11, 'TYR:plan': 8, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'ASN:plan1': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 299 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: "G" 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: "I" 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: "J" 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: "K" 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: "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: 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: "T" 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: "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: 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 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: 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: 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: "C" 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 Time building chain proxies: 7.38, per 1000 atoms: 0.25 Number of scatterers: 29444 At special positions: 0 Unit cell: (160.816, 168.222, 211.6, 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 5833 8.00 N 5018 7.00 C 18478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1201 " - " ASN A 709 " " NAG A1202 " - " ASN A1074 " " NAG A1203 " - " ASN A 61 " " NAG A1204 " - " ASN A 234 " " NAG A1205 " - " ASN A 603 " " NAG A1206 " - " ASN A 616 " " NAG A1207 " - " ASN A 657 " " NAG A1208 " - " ASN A 165 " " NAG B1201 " - " ASN B 616 " " NAG B1202 " - " ASN B 709 " " NAG B1203 " - " ASN B1074 " " NAG B1204 " - " ASN B 61 " " NAG B1205 " - " ASN B 122 " " NAG B1206 " - " ASN B 234 " " NAG B1207 " - " ASN B 603 " " NAG B1208 " - " ASN B 657 " " NAG B1209 " - " ASN B 165 " " NAG C1202 " - " ASN C 657 " " NAG C1203 " - " ASN C 122 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 616 " " NAG C1206 " - " ASN C 709 " " NAG C1207 " - " ASN C1074 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.6 seconds 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7934 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 66 sheets defined 21.4% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.637A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.014A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 426 through 430 removed outlier: 4.012A pdb=" N THR A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.730A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.512A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.645A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.617A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.685A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.590A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.593A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.681A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 968 " --> pdb=" O LYS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.589A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.597A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.741A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.658A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.798A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.434A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.763A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.738A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.745A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.667A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.585A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.268A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.776A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.710A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.528A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.744A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.801A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.798A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.800A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.183A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.770A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.831A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 64 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 187 through 191 Processing helix chain 'M' and resid 200 through 204 Processing helix chain 'N' and resid 140 through 144 removed outlier: 4.000A pdb=" N GLU N 143 " --> pdb=" O TYR N 140 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA N 144 " --> pdb=" O PRO N 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 140 through 144' Processing helix chain 'N' and resid 184 through 189 Processing helix chain 'P' and resid 26 through 31 Processing helix chain 'P' and resid 72 through 75 Processing helix chain 'P' and resid 100E through 100I removed outlier: 4.443A pdb=" N LEU P 100H" --> pdb=" O TYR P 100E" (cutoff:3.500A) Processing helix chain 'P' and resid 200 through 204 Processing helix chain 'O' and resid 49 through 52 Processing helix chain 'O' and resid 59 through 62 Processing helix chain 'O' and resid 121 through 131 removed outlier: 4.409A pdb=" N LEU O 125 " --> pdb=" O ASP O 122 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY O 128 " --> pdb=" O LEU O 125 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR O 129 " --> pdb=" O LYS O 126 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER O 131 " --> pdb=" O GLY O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 184 through 189 Processing helix chain 'H' and resid 60 through 65 removed outlier: 4.317A pdb=" N GLY H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 75 removed outlier: 4.223A pdb=" N SER H 74 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 189 Processing helix chain 'L' and resid 59 through 62 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 150 through 153 Processing helix chain 'L' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.263A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.024A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.925A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.942A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.699A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.080A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.006A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.865A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.865A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.670A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.128A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.691A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.315A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.088A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.840A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.942A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.597A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.675A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.534A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.783A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.247A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.615A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.567A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AE2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'M' and resid 9 through 12 removed outlier: 7.041A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 18 through 19 Processing sheet with id=AE5, first strand: chain 'M' and resid 50 through 51 Processing sheet with id=AE6, first strand: chain 'M' and resid 121 through 122 Processing sheet with id=AE7, first strand: chain 'M' and resid 137 through 138 removed outlier: 3.575A pdb=" N VAL M 181 " --> pdb=" O HIS M 164 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AE9, first strand: chain 'N' and resid 10 through 11 Processing sheet with id=AF1, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.535A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 134 through 139 removed outlier: 4.827A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 145 through 146 Processing sheet with id=AF4, first strand: chain 'N' and resid 191 through 193 Processing sheet with id=AF5, first strand: chain 'P' and resid 5 through 7 removed outlier: 3.734A pdb=" N VAL P 5 " --> pdb=" O GLN P 23 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU P 80 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 10 through 12 Processing sheet with id=AF7, first strand: chain 'P' and resid 56 through 59 removed outlier: 6.756A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE P 50 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE P 34 " --> pdb=" O ILE P 50 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR P 102 " --> pdb=" O ARG P 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 120 through 122 removed outlier: 3.847A pdb=" N SER P 120 " --> pdb=" O LYS P 143 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS P 143 " --> pdb=" O LEU P 178 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU P 178 " --> pdb=" O LYS P 143 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU P 175 " --> pdb=" O GLN P 171 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 137 through 139 Processing sheet with id=AG1, first strand: chain 'P' and resid 194 through 195 Processing sheet with id=AG2, first strand: chain 'O' and resid 5 through 6 Processing sheet with id=AG3, first strand: chain 'O' and resid 46 through 48 removed outlier: 6.781A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 134 through 136 removed outlier: 7.520A pdb=" N THR O 172 " --> pdb=" O GLN O 166 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN O 166 " --> pdb=" O THR O 172 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER O 174 " --> pdb=" O THR O 164 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 144 through 147 removed outlier: 4.413A pdb=" N GLU O 195 " --> pdb=" O GLN O 147 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 19 through 23 Processing sheet with id=AG7, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.407A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 120 through 123 Processing sheet with id=AG9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.505A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 132 through 135 Processing sheet with id=AH3, first strand: chain 'L' and resid 155 through 156 1182 hydrogen bonds defined for protein. 3075 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: 8.26 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4992 1.27 - 1.41: 7286 1.41 - 1.55: 17392 1.55 - 1.69: 144 1.69 - 1.82: 148 Bond restraints: 29962 Sorted by residual: bond pdb=" CA PRO O 119 " pdb=" C PRO O 119 " ideal model delta sigma weight residual 1.514 1.542 -0.027 5.50e-03 3.31e+04 2.46e+01 bond pdb=" C LYS M 214 " pdb=" O LYS M 214 " ideal model delta sigma weight residual 1.231 1.136 0.095 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C4 NAG T 2 " pdb=" O4 NAG T 2 " ideal model delta sigma weight residual 1.409 1.500 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C4 NAG R 2 " pdb=" O4 NAG R 2 " ideal model delta sigma weight residual 1.409 1.494 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C4 NAG K 2 " pdb=" O4 NAG K 2 " ideal model delta sigma weight residual 1.409 1.491 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 29957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 31102 2.22 - 4.43: 8997 4.43 - 6.65: 893 6.65 - 8.86: 74 8.86 - 11.08: 15 Bond angle restraints: 41081 Sorted by residual: angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 120.98 -7.18 1.00e+00 1.00e+00 5.16e+01 angle pdb=" N VAL A 289 " pdb=" CA VAL A 289 " pdb=" C VAL A 289 " ideal model delta sigma weight residual 111.90 117.33 -5.43 8.10e-01 1.52e+00 4.50e+01 angle pdb=" C SER B 45 " pdb=" N SER B 46 " pdb=" CA SER B 46 " ideal model delta sigma weight residual 120.90 129.92 -9.02 1.41e+00 5.03e-01 4.09e+01 angle pdb=" CA PHE A 643 " pdb=" CB PHE A 643 " pdb=" CG PHE A 643 " ideal model delta sigma weight residual 113.80 120.17 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" C LEU M 100G" pdb=" N LEU M 100H" pdb=" CA LEU M 100H" ideal model delta sigma weight residual 120.23 130.54 -10.31 1.67e+00 3.59e-01 3.81e+01 ... (remaining 41076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 17594 21.09 - 42.18: 710 42.18 - 63.27: 151 63.27 - 84.36: 106 84.36 - 105.44: 57 Dihedral angle restraints: 18618 sinusoidal: 6368 harmonic: 12250 Sorted by residual: dihedral pdb=" C LYS B 300 " pdb=" N LYS B 300 " pdb=" CA LYS B 300 " pdb=" CB LYS B 300 " ideal model delta harmonic sigma weight residual -122.60 -137.63 15.03 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" CA PHE M 146 " pdb=" C PHE M 146 " pdb=" N PRO M 147 " pdb=" CA PRO M 147 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASN P 56 " pdb=" C ASN P 56 " pdb=" N THR P 57 " pdb=" CA THR P 57 " ideal model delta harmonic sigma weight residual -180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 18615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 4944 0.214 - 0.428: 177 0.428 - 0.643: 5 0.643 - 0.857: 1 0.857 - 1.071: 4 Chirality restraints: 5131 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-02 2.50e+03 1.49e+03 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.09e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 ... (remaining 5128 not shown) Planarity restraints: 5419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " 0.261 2.00e-02 2.50e+03 1.44e-01 4.13e+02 pdb=" CG TYR A 904 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " -0.116 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " -0.135 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " -0.094 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " -0.073 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " 0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " 0.218 2.00e-02 2.50e+03 1.20e-01 2.88e+02 pdb=" CG TYR B 904 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " -0.112 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " -0.058 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " -0.197 2.00e-02 2.50e+03 1.02e-01 2.62e+02 pdb=" CG TRP A 886 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " 0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " 0.074 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.125 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " -0.138 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.068 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " -0.094 2.00e-02 2.50e+03 ... (remaining 5416 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 14962 2.99 - 3.47: 30271 3.47 - 3.95: 46781 3.95 - 4.42: 52279 4.42 - 4.90: 86446 Nonbonded interactions: 230739 Sorted by model distance: nonbonded pdb=" OE2 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.514 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.535 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.542 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.543 3.040 nonbonded pdb=" O5 NAG D 1 " pdb=" O6 NAG D 1 " model vdw 2.546 2.432 ... (remaining 230734 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 27 through 466 or resid 491 through 1207)) selection = (chain 'B' and (resid 27 through 466 or resid 491 through 1207)) selection = (chain 'C' and (resid 27 through 352 or (resid 353 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 through 395 \ or (resid 396 through 403 and (name N or name CA or name C or name O or name CB \ )) or resid 404 or (resid 405 through 411 and (name N or name CA or name C or n \ ame O or name CB )) or resid 412 through 413 or (resid 414 through 415 and (name \ N or name CA or name C or name O or name CB )) or resid 416 through 436 or (res \ id 437 through 445 and (name N or name CA or name C or name O or name CB )) or r \ esid 446 through 499 or (resid 500 through 501 and (name N or name CA or name C \ or name O or name CB )) or resid 502 or (resid 503 and (name N or name CA or nam \ e C or name O or name CB )) or resid 504 or (resid 505 through 506 and (name N o \ r name CA or name C or name O or name CB )) or resid 507 through 508 or (resid 5 \ 09 through 524 and (name N or name CA or name C or name O or name CB )) or resid \ 525 through 1207)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = (chain 'M' and (resid 1 through 98 or (resid 99 through 100A and (name N or name \ CA or name C or name O or name CB )) or resid 100B through 100E or (resid 100F \ through 100G and (name N or name CA or name C or name O or name CB )) or resid 1 \ 00H through 214)) selection = chain 'P' } ncs_group { reference = chain 'L' selection = (chain 'N' and (resid 1 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 76 or (resid 77 through 87 and (nam \ e N or name CA or name C or name O or name CB )) or resid 88 through 214)) selection = (chain 'O' and (resid 1 through 27E or resid 28 through 214)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.600 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.013 0.095 30061 Z= 0.790 Angle : 1.967 18.848 41344 Z= 1.271 Chirality : 0.103 1.071 5131 Planarity : 0.013 0.147 5382 Dihedral : 15.986 105.444 10582 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 1.61 % Allowed : 9.22 % Favored : 89.16 % Rotamer: Outliers : 2.35 % Allowed : 4.15 % Favored : 93.50 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.12), residues: 4153 helix: -1.16 (0.16), residues: 726 sheet: -0.88 (0.21), residues: 537 loop : -1.78 (0.11), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B1039 TYR 0.261 0.023 TYR A 904 PHE 0.153 0.016 PHE B 43 TRP 0.197 0.028 TRP A 886 HIS 0.017 0.005 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01309 (29962) covalent geometry : angle 1.92958 (41081) SS BOND : bond 0.01119 ( 34) SS BOND : angle 1.64237 ( 68) hydrogen bonds : bond 0.15299 ( 1171) hydrogen bonds : angle 9.16904 ( 3075) link_BETA1-4 : bond 0.03221 ( 28) link_BETA1-4 : angle 7.07155 ( 84) link_NAG-ASN : bond 0.01223 ( 37) link_NAG-ASN : angle 4.86736 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 1.081 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: symmetry clash REVERT: A 338 PHE cc_start: 0.9014 (m-10) cc_final: 0.8730 (m-10) REVERT: A 697 MET cc_start: 0.8539 (ptm) cc_final: 0.8335 (ptm) REVERT: B 43 PHE cc_start: 0.6256 (t80) cc_final: 0.5760 (t80) REVERT: B 603 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8474 (t0) REVERT: B 764 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8460 (m110) REVERT: C 353 TRP cc_start: 0.6840 (OUTLIER) cc_final: 0.6618 (t60) REVERT: C 869 MET cc_start: 0.8454 (mtt) cc_final: 0.7913 (mtt) REVERT: M 58 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9126 (mt) REVERT: P 100 SER cc_start: 0.6280 (OUTLIER) cc_final: 0.5967 (p) REVERT: O 4 MET cc_start: -0.0872 (mmt) cc_final: -0.1406 (tpp) REVERT: O 31 ASN cc_start: 0.4655 (OUTLIER) cc_final: 0.4439 (p0) REVERT: O 36 TYR cc_start: 0.4681 (OUTLIER) cc_final: 0.3388 (t80) REVERT: O 92 TYR cc_start: 0.5546 (t80) cc_final: 0.3328 (t80) REVERT: L 2 ILE cc_start: 0.3907 (OUTLIER) cc_final: 0.3500 (tt) REVERT: L 27 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7810 (pm20) outliers start: 56 outliers final: 10 residues processed: 200 average time/residue: 0.1801 time to fit residues: 60.1380 Evaluate side-chains 103 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain P residue 100 SER Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 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 935 GLN A1088 HIS B 606 ASN B 907 ASN B 919 ASN C 314 GLN C 317 ASN C 321 GLN C 919 ASN C 955 ASN C 957 GLN ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.085590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.058433 restraints weight = 146215.261| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 4.25 r_work: 0.3267 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30061 Z= 0.159 Angle : 0.813 17.848 41344 Z= 0.406 Chirality : 0.049 0.380 5131 Planarity : 0.005 0.058 5382 Dihedral : 11.749 75.150 5805 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.01 % Favored : 92.87 % Rotamer: Outliers : 1.47 % Allowed : 7.26 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.13), residues: 4153 helix: 0.67 (0.19), residues: 726 sheet: -1.23 (0.16), residues: 917 loop : -1.37 (0.12), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 77 TYR 0.026 0.002 TYR C 505 PHE 0.024 0.002 PHE A1089 TRP 0.020 0.002 TRP A1102 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00317 (29962) covalent geometry : angle 0.75054 (41081) SS BOND : bond 0.00387 ( 34) SS BOND : angle 1.92551 ( 68) hydrogen bonds : bond 0.04566 ( 1171) hydrogen bonds : angle 7.00928 ( 3075) link_BETA1-4 : bond 0.01748 ( 28) link_BETA1-4 : angle 5.23806 ( 84) link_NAG-ASN : bond 0.00596 ( 37) link_NAG-ASN : angle 3.83676 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.9297 (m-10) cc_final: 0.9034 (m-10) REVERT: A 740 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8400 (ttm) REVERT: A 762 GLN cc_start: 0.9242 (tt0) cc_final: 0.9002 (tp40) REVERT: B 324 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: B 1132 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8571 (mm) REVERT: C 353 TRP cc_start: 0.7032 (OUTLIER) cc_final: 0.6729 (t60) REVERT: C 374 PHE cc_start: 0.8733 (m-10) cc_final: 0.8506 (m-10) REVERT: M 52 TYR cc_start: 0.8966 (t80) cc_final: 0.8759 (t80) REVERT: M 58 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9181 (mt) REVERT: N 27 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.7998 (pp30) REVERT: O 4 MET cc_start: 0.2238 (mmt) cc_final: 0.1042 (tpp) REVERT: O 27 TYR cc_start: 0.7676 (t80) cc_final: 0.7200 (m-80) REVERT: O 36 TYR cc_start: 0.4577 (OUTLIER) cc_final: 0.3735 (t80) REVERT: L 2 ILE cc_start: 0.4378 (OUTLIER) cc_final: 0.4007 (tt) outliers start: 35 outliers final: 12 residues processed: 127 average time/residue: 0.1673 time to fit residues: 37.3094 Evaluate side-chains 102 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 2 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 63 optimal weight: 0.9980 chunk 282 optimal weight: 8.9990 chunk 300 optimal weight: 0.0980 chunk 248 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 291 optimal weight: 40.0000 chunk 166 optimal weight: 4.9990 chunk 330 optimal weight: 20.0000 chunk 345 optimal weight: 50.0000 chunk 308 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A1058 HIS B 907 ASN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.085426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.057843 restraints weight = 146810.282| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 4.57 r_work: 0.3273 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30061 Z= 0.136 Angle : 0.697 18.118 41344 Z= 0.340 Chirality : 0.047 0.375 5131 Planarity : 0.004 0.058 5382 Dihedral : 8.674 58.086 5786 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.75 % Favored : 92.20 % Rotamer: Outliers : 1.01 % Allowed : 8.64 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4153 helix: 1.22 (0.20), residues: 727 sheet: -1.30 (0.16), residues: 925 loop : -1.17 (0.12), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.023 0.001 TYR A1067 PHE 0.020 0.002 PHE B 106 TRP 0.020 0.001 TRP B 104 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00284 (29962) covalent geometry : angle 0.64387 (41081) SS BOND : bond 0.00333 ( 34) SS BOND : angle 1.15673 ( 68) hydrogen bonds : bond 0.03744 ( 1171) hydrogen bonds : angle 6.28799 ( 3075) link_BETA1-4 : bond 0.01609 ( 28) link_BETA1-4 : angle 4.98280 ( 84) link_NAG-ASN : bond 0.00445 ( 37) link_NAG-ASN : angle 2.81326 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.039 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 41 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8425 (mmmt) REVERT: A 338 PHE cc_start: 0.9333 (m-10) cc_final: 0.9063 (m-10) REVERT: A 762 GLN cc_start: 0.9223 (tt0) cc_final: 0.9000 (tp40) REVERT: B 43 PHE cc_start: 0.6590 (t80) cc_final: 0.6378 (t80) REVERT: B 287 ASP cc_start: 0.8621 (t0) cc_final: 0.7926 (m-30) REVERT: C 353 TRP cc_start: 0.7006 (OUTLIER) cc_final: 0.6708 (t60) REVERT: M 58 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9059 (mm) REVERT: O 27 TYR cc_start: 0.7539 (t80) cc_final: 0.6752 (m-80) REVERT: O 92 TYR cc_start: 0.5607 (t80) cc_final: 0.5318 (t80) REVERT: L 27 LEU cc_start: 0.9302 (mt) cc_final: 0.8929 (mt) REVERT: L 92 TYR cc_start: 0.8429 (t80) cc_final: 0.8189 (t80) outliers start: 24 outliers final: 13 residues processed: 111 average time/residue: 0.1702 time to fit residues: 32.8354 Evaluate side-chains 92 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 337 optimal weight: 40.0000 chunk 168 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 24 optimal weight: 30.0000 chunk 196 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 402 optimal weight: 40.0000 chunk 195 optimal weight: 9.9990 chunk 297 optimal weight: 30.0000 chunk 397 optimal weight: 9.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 755 GLN B 901 GLN B 907 ASN B1005 GLN C 606 ASN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.083042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.054335 restraints weight = 147751.267| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 4.29 r_work: 0.3145 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.136 30061 Z= 0.380 Angle : 0.841 18.823 41344 Z= 0.414 Chirality : 0.051 0.360 5131 Planarity : 0.005 0.055 5382 Dihedral : 7.906 56.463 5781 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.99 % Favored : 91.98 % Rotamer: Outliers : 2.06 % Allowed : 9.61 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 4153 helix: 0.85 (0.19), residues: 731 sheet: -1.44 (0.16), residues: 995 loop : -1.32 (0.13), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1039 TYR 0.030 0.003 TYR A1067 PHE 0.040 0.003 PHE A1089 TRP 0.016 0.002 TRP A1102 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00855 (29962) covalent geometry : angle 0.79730 (41081) SS BOND : bond 0.00609 ( 34) SS BOND : angle 1.79659 ( 68) hydrogen bonds : bond 0.04298 ( 1171) hydrogen bonds : angle 6.58518 ( 3075) link_BETA1-4 : bond 0.01456 ( 28) link_BETA1-4 : angle 4.92595 ( 84) link_NAG-ASN : bond 0.00664 ( 37) link_NAG-ASN : angle 2.84180 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 78 time to evaluate : 1.262 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 338 PHE cc_start: 0.9332 (m-10) cc_final: 0.9073 (m-10) REVERT: A 762 GLN cc_start: 0.9256 (tt0) cc_final: 0.9016 (tp40) REVERT: A 1032 CYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7446 (m) REVERT: B 43 PHE cc_start: 0.6799 (t80) cc_final: 0.6030 (m-80) REVERT: B 102 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7155 (mpt180) REVERT: B 324 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8423 (pm20) REVERT: B 1101 HIS cc_start: 0.5810 (OUTLIER) cc_final: 0.4217 (m90) REVERT: M 58 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9043 (mt) REVERT: N 32 TYR cc_start: 0.8691 (m-10) cc_final: 0.8082 (m-10) REVERT: O 27 TYR cc_start: 0.7472 (t80) cc_final: 0.7003 (m-80) outliers start: 49 outliers final: 27 residues processed: 118 average time/residue: 0.1714 time to fit residues: 35.1715 Evaluate side-chains 106 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain N residue 9 ASP Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 412 optimal weight: 10.0000 chunk 303 optimal weight: 50.0000 chunk 288 optimal weight: 0.5980 chunk 279 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 48 optimal weight: 0.0770 chunk 269 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 295 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 901 GLN B 907 ASN B1088 HIS C 540 ASN C 901 GLN N 42 GLN L 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.085014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.057240 restraints weight = 146744.884| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.61 r_work: 0.3256 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30061 Z= 0.116 Angle : 0.647 18.204 41344 Z= 0.316 Chirality : 0.046 0.353 5131 Planarity : 0.004 0.060 5382 Dihedral : 7.182 58.989 5781 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.10 % Favored : 92.87 % Rotamer: Outliers : 1.38 % Allowed : 10.28 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 4153 helix: 1.52 (0.20), residues: 707 sheet: -1.26 (0.16), residues: 979 loop : -1.12 (0.13), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1107 TYR 0.020 0.001 TYR A 904 PHE 0.025 0.001 PHE C 220 TRP 0.016 0.001 TRP B 104 HIS 0.002 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00235 (29962) covalent geometry : angle 0.59582 (41081) SS BOND : bond 0.00329 ( 34) SS BOND : angle 1.80669 ( 68) hydrogen bonds : bond 0.03447 ( 1171) hydrogen bonds : angle 5.95926 ( 3075) link_BETA1-4 : bond 0.01516 ( 28) link_BETA1-4 : angle 4.66310 ( 84) link_NAG-ASN : bond 0.00435 ( 37) link_NAG-ASN : angle 2.50800 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 1.223 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 41 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8370 (mmmt) REVERT: A 338 PHE cc_start: 0.9354 (m-10) cc_final: 0.9085 (m-10) REVERT: B 43 PHE cc_start: 0.6631 (t80) cc_final: 0.5954 (m-80) REVERT: B 104 TRP cc_start: 0.7440 (m-90) cc_final: 0.7180 (m-90) REVERT: B 287 ASP cc_start: 0.8598 (t0) cc_final: 0.7983 (m-30) REVERT: B 324 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: B 488 CYS cc_start: 0.6032 (OUTLIER) cc_final: 0.4958 (t) REVERT: B 543 PHE cc_start: 0.7763 (t80) cc_final: 0.7532 (t80) REVERT: B 1101 HIS cc_start: 0.5770 (OUTLIER) cc_final: 0.4048 (m90) REVERT: C 353 TRP cc_start: 0.6988 (OUTLIER) cc_final: 0.6496 (t60) REVERT: C 1101 HIS cc_start: 0.5018 (OUTLIER) cc_final: 0.4647 (m170) REVERT: M 58 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8969 (mm) REVERT: N 4 MET cc_start: 0.7410 (mtm) cc_final: 0.7205 (mtm) REVERT: N 32 TYR cc_start: 0.8733 (m-10) cc_final: 0.8252 (m-10) REVERT: O 27 TYR cc_start: 0.7546 (t80) cc_final: 0.6956 (m-80) REVERT: O 92 TYR cc_start: 0.6008 (t80) cc_final: 0.5344 (t80) outliers start: 33 outliers final: 15 residues processed: 112 average time/residue: 0.1764 time to fit residues: 34.0970 Evaluate side-chains 102 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 42 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 88 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 217 optimal weight: 9.9990 chunk 302 optimal weight: 40.0000 chunk 385 optimal weight: 50.0000 chunk 282 optimal weight: 0.9980 chunk 420 optimal weight: 50.0000 chunk 100 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 321 optimal weight: 40.0000 chunk 298 optimal weight: 20.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN C 901 GLN N 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.084097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.055602 restraints weight = 147558.879| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 4.48 r_work: 0.3191 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 30061 Z= 0.236 Angle : 0.685 18.423 41344 Z= 0.334 Chirality : 0.046 0.351 5131 Planarity : 0.004 0.055 5382 Dihedral : 7.103 59.910 5781 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.61 % Favored : 92.34 % Rotamer: Outliers : 1.43 % Allowed : 10.74 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4153 helix: 1.40 (0.20), residues: 726 sheet: -1.26 (0.16), residues: 1013 loop : -1.14 (0.13), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.024 0.002 TYR A1067 PHE 0.030 0.002 PHE C 220 TRP 0.010 0.001 TRP A1102 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00528 (29962) covalent geometry : angle 0.63984 (41081) SS BOND : bond 0.00318 ( 34) SS BOND : angle 1.48103 ( 68) hydrogen bonds : bond 0.03568 ( 1171) hydrogen bonds : angle 6.01806 ( 3075) link_BETA1-4 : bond 0.01452 ( 28) link_BETA1-4 : angle 4.55848 ( 84) link_NAG-ASN : bond 0.00437 ( 37) link_NAG-ASN : angle 2.44954 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8371 (mmmt) REVERT: B 43 PHE cc_start: 0.6693 (t80) cc_final: 0.6016 (m-80) REVERT: B 287 ASP cc_start: 0.8635 (t0) cc_final: 0.7973 (m-30) REVERT: B 324 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8525 (pm20) REVERT: B 543 PHE cc_start: 0.7632 (t80) cc_final: 0.7336 (t80) REVERT: B 902 MET cc_start: 0.9026 (tpp) cc_final: 0.8823 (mmt) REVERT: B 1101 HIS cc_start: 0.5807 (OUTLIER) cc_final: 0.4070 (m90) REVERT: C 1101 HIS cc_start: 0.5108 (OUTLIER) cc_final: 0.4714 (m170) REVERT: M 58 ILE cc_start: 0.9258 (mm) cc_final: 0.8936 (mm) REVERT: N 32 TYR cc_start: 0.8805 (m-10) cc_final: 0.8344 (m-10) REVERT: O 4 MET cc_start: 0.4475 (OUTLIER) cc_final: 0.3913 (ptm) REVERT: O 27 TYR cc_start: 0.7649 (t80) cc_final: 0.7257 (m-80) REVERT: L 2 ILE cc_start: 0.3892 (OUTLIER) cc_final: 0.3405 (tt) outliers start: 34 outliers final: 20 residues processed: 107 average time/residue: 0.1731 time to fit residues: 32.4401 Evaluate side-chains 103 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 5 optimal weight: 8.9990 chunk 388 optimal weight: 50.0000 chunk 86 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 398 optimal weight: 50.0000 chunk 318 optimal weight: 50.0000 chunk 402 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 907 ASN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.083756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.056710 restraints weight = 146168.247| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 4.00 r_work: 0.3207 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30061 Z= 0.180 Angle : 0.644 18.507 41344 Z= 0.313 Chirality : 0.045 0.348 5131 Planarity : 0.004 0.059 5382 Dihedral : 6.917 57.828 5779 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.44 % Favored : 92.54 % Rotamer: Outliers : 1.47 % Allowed : 11.08 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 4153 helix: 1.49 (0.20), residues: 721 sheet: -1.23 (0.16), residues: 1011 loop : -1.08 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.021 0.001 TYR A1067 PHE 0.024 0.002 PHE C 220 TRP 0.010 0.001 TRP A 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00399 (29962) covalent geometry : angle 0.59863 (41081) SS BOND : bond 0.00271 ( 34) SS BOND : angle 1.32120 ( 68) hydrogen bonds : bond 0.03416 ( 1171) hydrogen bonds : angle 5.88250 ( 3075) link_BETA1-4 : bond 0.01496 ( 28) link_BETA1-4 : angle 4.46860 ( 84) link_NAG-ASN : bond 0.00386 ( 37) link_NAG-ASN : angle 2.36148 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 1.109 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 41 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8454 (mmmt) REVERT: B 43 PHE cc_start: 0.6604 (t80) cc_final: 0.6039 (m-80) REVERT: B 287 ASP cc_start: 0.8600 (t0) cc_final: 0.8014 (m-30) REVERT: B 324 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8587 (pm20) REVERT: B 1101 HIS cc_start: 0.5820 (OUTLIER) cc_final: 0.4017 (m90) REVERT: C 207 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7377 (t-170) REVERT: C 912 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.7905 (p) REVERT: C 1101 HIS cc_start: 0.5157 (OUTLIER) cc_final: 0.4747 (m170) REVERT: C 1106 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7991 (pt0) REVERT: M 58 ILE cc_start: 0.9303 (mm) cc_final: 0.9005 (mm) REVERT: N 4 MET cc_start: 0.7697 (mtm) cc_final: 0.7485 (mtm) REVERT: N 32 TYR cc_start: 0.8660 (m-10) cc_final: 0.8255 (m-10) REVERT: O 4 MET cc_start: 0.2879 (OUTLIER) cc_final: 0.2123 (ptm) REVERT: O 27 TYR cc_start: 0.7623 (t80) cc_final: 0.7211 (m-80) REVERT: L 27 LEU cc_start: 0.9300 (mt) cc_final: 0.9043 (mt) REVERT: L 92 TYR cc_start: 0.8641 (t80) cc_final: 0.8413 (t80) outliers start: 35 outliers final: 17 residues processed: 109 average time/residue: 0.1664 time to fit residues: 32.1026 Evaluate side-chains 102 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 228 optimal weight: 0.8980 chunk 330 optimal weight: 50.0000 chunk 103 optimal weight: 3.9990 chunk 389 optimal weight: 50.0000 chunk 53 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 399 optimal weight: 3.9990 chunk 325 optimal weight: 40.0000 chunk 46 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.084294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.056264 restraints weight = 147552.464| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.12 r_work: 0.3193 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30061 Z= 0.195 Angle : 0.647 18.254 41344 Z= 0.315 Chirality : 0.045 0.346 5131 Planarity : 0.004 0.056 5382 Dihedral : 6.847 58.912 5779 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.61 % Favored : 92.37 % Rotamer: Outliers : 1.47 % Allowed : 11.29 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 4153 helix: 1.54 (0.20), residues: 715 sheet: -1.23 (0.16), residues: 1004 loop : -1.07 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.022 0.001 TYR A1067 PHE 0.022 0.002 PHE C 220 TRP 0.009 0.001 TRP A 104 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00433 (29962) covalent geometry : angle 0.60430 (41081) SS BOND : bond 0.00295 ( 34) SS BOND : angle 1.23537 ( 68) hydrogen bonds : bond 0.03414 ( 1171) hydrogen bonds : angle 5.85849 ( 3075) link_BETA1-4 : bond 0.01466 ( 28) link_BETA1-4 : angle 4.39732 ( 84) link_NAG-ASN : bond 0.00392 ( 37) link_NAG-ASN : angle 2.31356 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 1.140 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 41 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8464 (mmmt) REVERT: A 567 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8309 (tpp80) REVERT: B 43 PHE cc_start: 0.6598 (t80) cc_final: 0.6009 (m-80) REVERT: B 287 ASP cc_start: 0.8595 (t0) cc_final: 0.8022 (m-30) REVERT: B 324 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: B 902 MET cc_start: 0.8990 (tpp) cc_final: 0.8582 (mmt) REVERT: B 1101 HIS cc_start: 0.5843 (OUTLIER) cc_final: 0.4043 (m90) REVERT: C 207 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7290 (t-170) REVERT: C 912 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.7927 (p) REVERT: C 1101 HIS cc_start: 0.5170 (OUTLIER) cc_final: 0.4764 (m170) REVERT: C 1106 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: M 58 ILE cc_start: 0.9280 (mm) cc_final: 0.8990 (mm) REVERT: M 100 LEU cc_start: 0.8028 (mm) cc_final: 0.7790 (tt) REVERT: N 32 TYR cc_start: 0.8882 (m-10) cc_final: 0.8420 (m-10) REVERT: O 4 MET cc_start: 0.3140 (OUTLIER) cc_final: 0.2438 (ptm) REVERT: O 27 TYR cc_start: 0.7634 (t80) cc_final: 0.7240 (m-80) REVERT: L 2 ILE cc_start: 0.3746 (OUTLIER) cc_final: 0.3368 (tt) REVERT: L 27 LEU cc_start: 0.9351 (mt) cc_final: 0.9100 (mt) outliers start: 35 outliers final: 19 residues processed: 109 average time/residue: 0.1681 time to fit residues: 32.2163 Evaluate side-chains 105 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 19 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 411 optimal weight: 50.0000 chunk 16 optimal weight: 8.9990 chunk 385 optimal weight: 40.0000 chunk 308 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 344 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C 907 ASN O 29 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.084368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.056096 restraints weight = 147229.344| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.33 r_work: 0.3201 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30061 Z= 0.187 Angle : 0.639 18.412 41344 Z= 0.311 Chirality : 0.045 0.344 5131 Planarity : 0.004 0.059 5382 Dihedral : 6.745 57.247 5779 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.39 % Favored : 92.58 % Rotamer: Outliers : 1.26 % Allowed : 11.54 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4153 helix: 1.61 (0.20), residues: 701 sheet: -1.27 (0.16), residues: 1014 loop : -1.04 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.022 0.001 TYR A1067 PHE 0.020 0.002 PHE B 559 TRP 0.009 0.001 TRP A 104 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00416 (29962) covalent geometry : angle 0.59524 (41081) SS BOND : bond 0.00365 ( 34) SS BOND : angle 1.53939 ( 68) hydrogen bonds : bond 0.03398 ( 1171) hydrogen bonds : angle 5.79718 ( 3075) link_BETA1-4 : bond 0.01484 ( 28) link_BETA1-4 : angle 4.32267 ( 84) link_NAG-ASN : bond 0.00377 ( 37) link_NAG-ASN : angle 2.27133 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 1.089 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 41 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8438 (mmmt) REVERT: A 567 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8210 (tpp80) REVERT: B 43 PHE cc_start: 0.6623 (t80) cc_final: 0.6050 (m-80) REVERT: B 287 ASP cc_start: 0.8636 (t0) cc_final: 0.8004 (m-30) REVERT: B 324 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8638 (pm20) REVERT: B 902 MET cc_start: 0.9067 (tpp) cc_final: 0.8633 (mmt) REVERT: B 1101 HIS cc_start: 0.6001 (OUTLIER) cc_final: 0.4198 (m90) REVERT: C 912 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.7959 (p) REVERT: C 1101 HIS cc_start: 0.5185 (OUTLIER) cc_final: 0.4730 (m170) REVERT: C 1106 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: M 58 ILE cc_start: 0.9248 (mm) cc_final: 0.8967 (mm) REVERT: M 100 LEU cc_start: 0.8055 (mm) cc_final: 0.7778 (tt) REVERT: N 32 TYR cc_start: 0.8978 (m-10) cc_final: 0.8508 (m-10) REVERT: O 4 MET cc_start: 0.3821 (OUTLIER) cc_final: 0.3306 (ptm) REVERT: O 27 TYR cc_start: 0.7627 (t80) cc_final: 0.7399 (m-80) REVERT: L 2 ILE cc_start: 0.3781 (OUTLIER) cc_final: 0.3420 (tt) REVERT: L 27 LEU cc_start: 0.9315 (mt) cc_final: 0.9097 (mt) outliers start: 30 outliers final: 20 residues processed: 102 average time/residue: 0.1692 time to fit residues: 30.3839 Evaluate side-chains 104 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 194 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 265 optimal weight: 0.6980 chunk 317 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 326 optimal weight: 40.0000 chunk 331 optimal weight: 8.9990 chunk 268 optimal weight: 0.4980 chunk 374 optimal weight: 50.0000 chunk 172 optimal weight: 0.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.084162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.055852 restraints weight = 146681.119| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 4.42 r_work: 0.3185 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30061 Z= 0.201 Angle : 0.643 18.355 41344 Z= 0.313 Chirality : 0.045 0.343 5131 Planarity : 0.004 0.056 5382 Dihedral : 6.710 57.895 5779 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.66 % Favored : 92.32 % Rotamer: Outliers : 1.26 % Allowed : 11.50 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 4153 helix: 1.65 (0.20), residues: 691 sheet: -1.28 (0.16), residues: 1019 loop : -1.03 (0.13), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.022 0.001 TYR A1067 PHE 0.021 0.002 PHE B 559 TRP 0.008 0.001 TRP H 100B HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00447 (29962) covalent geometry : angle 0.60030 (41081) SS BOND : bond 0.00288 ( 34) SS BOND : angle 1.66545 ( 68) hydrogen bonds : bond 0.03399 ( 1171) hydrogen bonds : angle 5.78240 ( 3075) link_BETA1-4 : bond 0.01453 ( 28) link_BETA1-4 : angle 4.26085 ( 84) link_NAG-ASN : bond 0.00405 ( 37) link_NAG-ASN : angle 2.24240 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 1.158 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: A 41 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8357 (mmmt) REVERT: A 567 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8186 (tpp80) REVERT: B 43 PHE cc_start: 0.6695 (t80) cc_final: 0.6130 (m-80) REVERT: B 287 ASP cc_start: 0.8641 (t0) cc_final: 0.8011 (m-30) REVERT: B 324 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8694 (pm20) REVERT: B 902 MET cc_start: 0.9060 (tpp) cc_final: 0.8617 (mmt) REVERT: B 1101 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.4349 (m90) REVERT: C 912 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.7984 (p) REVERT: C 1101 HIS cc_start: 0.5232 (OUTLIER) cc_final: 0.4738 (m170) REVERT: C 1106 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: M 58 ILE cc_start: 0.9274 (mm) cc_final: 0.9007 (mm) REVERT: M 100 LEU cc_start: 0.8005 (mm) cc_final: 0.7729 (tt) REVERT: N 32 TYR cc_start: 0.8998 (m-10) cc_final: 0.8520 (m-10) REVERT: O 4 MET cc_start: 0.3997 (OUTLIER) cc_final: 0.3522 (ptt) REVERT: O 27 TYR cc_start: 0.7720 (t80) cc_final: 0.7216 (m-80) REVERT: O 29 ASN cc_start: 0.9033 (t0) cc_final: 0.8796 (m110) REVERT: L 2 ILE cc_start: 0.3526 (OUTLIER) cc_final: 0.3240 (tt) REVERT: L 27 LEU cc_start: 0.9332 (mt) cc_final: 0.9114 (mt) outliers start: 30 outliers final: 20 residues processed: 106 average time/residue: 0.1695 time to fit residues: 31.2585 Evaluate side-chains 107 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 94 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 239 optimal weight: 5.9990 chunk 282 optimal weight: 8.9990 chunk 296 optimal weight: 30.0000 chunk 187 optimal weight: 7.9990 chunk 122 optimal weight: 50.0000 chunk 104 optimal weight: 30.0000 chunk 317 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.079932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.053301 restraints weight = 142346.499| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.06 r_work: 0.3159 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 30061 Z= 0.342 Angle : 0.760 18.903 41344 Z= 0.373 Chirality : 0.048 0.345 5131 Planarity : 0.005 0.059 5382 Dihedral : 7.111 57.247 5779 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.74 % Favored : 91.24 % Rotamer: Outliers : 1.43 % Allowed : 11.71 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.13), residues: 4153 helix: 1.26 (0.20), residues: 703 sheet: -1.44 (0.16), residues: 1007 loop : -1.17 (0.13), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1107 TYR 0.031 0.002 TYR B1067 PHE 0.034 0.003 PHE A1089 TRP 0.012 0.002 TRP B 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00762 (29962) covalent geometry : angle 0.72294 (41081) SS BOND : bond 0.00410 ( 34) SS BOND : angle 1.84208 ( 68) hydrogen bonds : bond 0.03906 ( 1171) hydrogen bonds : angle 6.14495 ( 3075) link_BETA1-4 : bond 0.01487 ( 28) link_BETA1-4 : angle 4.29555 ( 84) link_NAG-ASN : bond 0.00676 ( 37) link_NAG-ASN : angle 2.42790 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9453.60 seconds wall clock time: 161 minutes 35.90 seconds (9695.90 seconds total)